disease | ConservationBytes.com

Who are the healthiest people in the world?

8 05 2017

healthy Apologies for the little gap in my regular posts — I am in the fortunate position of having spent the last three weeks in the beautiful Villa Serbelloni in the village of Bellagio on the shores of Lake Como (northern Italy) engaged in writing a new book with my good friend and colleague, Professor Paul Ehrlich. Both of us received an invitation to become ‘Bellagio Centre Residents‘ by the Rockefeller Foundation to write the book in, shall we say, rather lush circumstances.

While I can’t yet give away all the juicy details of the book itself (we’ve only written about a third of it so far), I wanted to give you a little taste of some of the interesting results we’ve so far put together.

Today’s topic is on human health, which as I’ve written many times before, is in many ways linked to the quality of the environment in which people live. We are currently looking at which countries have the best human health statistics, as well as the best environmental conditions in which to live. Read the rest of this entry »

Comments : 1 Comment »
Tags: air quality, death, environment, health, health care, human health, investment, life expectancy, medical, mortality, survival
Categories : biowealth, disease, economics, health

InvaCost – estimating the economic damage of invasive insects

7 11 2014

This is a blosh (rehash of someone else’s blog post) of Franck Courchamp‘s posts on an exciting new initiative of which I am excited to be a part. Incidentally, Franck’s spending the week here in Adelaide.

Don’t forgot to vote for the project to receive 50 000 € public-communication grant!

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Climate change will make winters milder and habitats climatically more suitable year-round for cold-blooded animals like insects, but there are many questions remaining regarding whether such insects will be able to invade other regions as the climate shifts. There are many nasty bugs out there.

For example, the Asian predatory wasp is an invasive hornet in Europe that butchers pollinating insects, especially bees, thereby affecting the production of many wild and cultivated plants. I hope that we all remember what Einstein said about pollinators:

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

(we all should remember that because it’s one of the few things he said that most of us understood). The highly invasive red fire ant is feared for its impacts on biodiversity, agriculture and cattle breeding, and the thousands of anaphylactic shocks inflicted to people by painful stings every year (with hundreds of deaths). Between the USA and Australia, over US$10 billion is spent yearly on the control of this insect alone. Tiger mosquitoes are vectors of pathogens that cause dengue fever, chikungunya virus and of about 30 other viruses. We could go on.

Most of these nasty creatures are now unable to colonise northern regions of Europe or America, or southern regions of Australia, for example, because they cannot survive cold temperatures. But how will this change? Where, when and which species will invade with rising temperatures? What will be the costs in terms of species loss? In terms of agricultural or forestry loss? In terms of diseases to cattle, domestic animals and humans? What will be the death toll if insects that are vectors of malaria can establish in new, highly populated areas?

We’ve proposed to study these and others from a list of 20 of the worst invasive insect species worldwide, and we got selected (i.e., financed!) by the Fondation BNP Paribas. In addition, the Fondation BNP Paribas has selected five scientific programmes on climate change and will give 50,000 € (that’s US$62,000) to the one selected by the public, for a communication project on their scientific programme. This is why we need you to vote for our project: InvaCost. Read the rest of this entry »

Comments : 3 Comments »
Tags: BNP Paribas, Citizen science, climate change, Economics, Franck Courchamp, Global warming, insects, InvaCost, invasive species
Categories : agriculture, alien species, bioclimatic envelope, cattle, citizen science, climate change, climate shift, conservation, disease, ecology, economics, ecosystem, ecosystem services, environmental economics, Europe, food, health, invasive species, management, research, science, science communication

If biodiversity is so important, why is Europe not languishing?

17 03 2014

I don’t often respond to many comments on this blog unless they are really, really good questions (and if I think I have the answers). Even rarer is devoting an entire post to answering a question. The other day, I received a real cracker, and so I think it deserves a highlighted response.

Two days ago, a certain ‘P. Basu’ asked this in response to my last blog post (Lose biodiversity and you’ll get sick):

I am an Indian who lived in Germany for quite a long period. Now, if I am not grossly mistaken, once upon a time Germany and other west european countries had large tracts of “real” forests with bears, wolves, foxes and other animals (both carnivore and herbivore). Bear has completely disappeared from these countries with the advent of industrialization. A few wolves have been kept in more or less artificially created forests. Foxes, deer and hares, fortunately, do still exist. My question is, how come these countries are still so well off – not only from the point of view of economy but also from the angle of public health despite the loss of large tracts of natural forests? Or is it that modern science and a health conscious society can compensate the loss of biodiversity.

“Well”, I thought to myself, “Bloody good question”.

I have come across this genre of question before, but usually under more hostile circumstances when an overtly right-wing respondent (hell, let’s call a spade a spade – a ‘completely selfish arsehole’) has challenged me on the ‘value of nature’ logic (I’m not for a moment suggesting that P. Basu is this sort of person; on the contrary, he politely asked an extremely important question that requires an answer). The comeback generally goes something like this: “If biodiversity is so important, why aren’t super-developed countries wallowing in economic and social ruin because they’ve degraded their own life-support systems? Clearly you must be wrong, Sir.”

There have been discussions in the ecological and sustainability literature that have attempted to answer this, but I’ll give it a shot here for the benefit of CB.com readers. Read the rest of this entry »

Comments : 11 Comments »
Tags: biodiversity, biowealth, decline, Economics, ecosystem services, society
Categories : agriculture, anthropocene, Asia, Australia, biodiversity, Central America, China, conservation, decline, deforestation, disease, economics, ecosystem services, environmental policy, extinction, extinction debt, food, habitat loss, health, human overpopulation, pollution, poverty, South America, tropical

Lose biodiversity and you’ll get sick

14 03 2014

Here’s a (paraphrased) recommendation I did recently for F1000 about a cool avenue of research I’ve been following for a few years now. Very interesting, but much, much more to do.

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The core concepts of conservation ecology are well-established: we know that habitat loss, fragmentation, invasive species, over-exploitation and of course, climate change, are bad for biodiversity. This well-quantified scientific baseline has led the discipline recently to embark on questions pertaining more to the (a) implications of biodiversity loss for humanity and (b) what we can do to offset these. A recent paper by Morand and colleagues addresses perhaps one of the most compelling reasons that human society should appreciate biodiversity beyond its intrinsic value; as biodiversity degrades, so too does human health.

Some argue that the only way to convince society in general that biodiversity is worth protecting is that we link its loss directly to degrading human health, wealth and well-being. Confirmation of such relationships at a variety of spatial and temporal scales is therefore essential. Morand and colleagues used data from a variety of sources to test two predictions: (1) that the number of infectious disease should increase as overall biodiversity increases and (2) that biodiversity loss, inferred from species threat and deforestation data, should increase the number of infectious disease outbreaks in humans. Using data from 28 countries in the Asia-Pacific region, they confirmed both predictions. Read the rest of this entry »

Comments : 7 Comments »
Tags: biodiversity, disease, EID, environment, human health, ID, infectious, sick
Categories : agriculture, biodiversity, climate change, conservation, decline, deforestation, disease, ecosystem function, ecosystem services, fragmentation, habitat loss, malaria

More species = more resilience

8 01 2014

While still ostensibly ‘on leave’ (side note: Does any scientist really ever take a proper holiday? Perhaps a subject for a future blog post), I cannot resist the temptation to blog about our lab’s latest paper that just came online today. In particular, I am particularly proud of Dr Camille Mellin, lead author of the study and all-round kick-arse quantitative ecologist, who has outdone herself on this one.

Today’s subject is one I’ve touched on before, but to my knowledge, the relationship between ‘diversity’ (simply put, ‘more species’) and ecosystem resilience (i.e., resisting extinction) has never been demonstrated so elegantly. Not only is the study elegant (admission: I am a co-author and therefore my opinion is likely to be biased toward the positive), it demonstrates the biodiversity-stability hypothesis in a natural setting (not experimental) over a range of thousands of kilometres. Finally, there’s an interesting little twist at the end demonstrating yet again that ecology is more complex than rocket science.

Despite a legacy of debate, the so-called diversity-stability hypothesis is now a widely used rule of thumb, and its even implicit in most conservation planning tools (i.e., set aside areas with more species because we assume more is better). Why should ‘more’ be ‘better’? Well, when a lot of species are interacting and competing in an ecosystem, the ‘average’ interactions that any one species experiences are likely to be weaker than in a simpler, less diverse system. When there are a lot of different niches occupied by different species, we also expect different responses to environmental fluctuations among the community, meaning that some species inherently do better than others depending on the specific disturbance. Species-rich systems also tend to have more of what we call ‘functional redundancy‘, meaning that if one species providing an essential ecosystem function (e.g., like predation) goes extinct, there’s another, similar species ready to take its place. Read the rest of this entry »

Comments : 10 Comments »
Tags: beta diversity, coral reef, diversity-stability, ecology, fluctuation, metacommunity, metapopulation, portfolio effect, reef fish, resilience
Categories : algae, alien species, Australia, biodiversity, climate change, coasts, connectivity, conservation, coral reefs, disease, ecology, ecosystem, ecosystem function, endemic, endemism, extinction, fish, function, invasive species, marine, marine protected area, metapopulation, planning, predator, prioritisation, protected area, recovery, reserve, shark, tropical

Cleaning up the rubbish: Australian megafauna extinctions

15 11 2013

A 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), geneticists, 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 »

Comments : 5 Comments »
Tags: Ancient DNA, Australasia, Australia, climate change, Extinctions, Fossil, hunting, megafauna, over-exploitation, Sahul
Categories : Australia, climate change, conservation, disease, DNA, exploitation, extinction, genetics, harvest, mathematics, metapopulation, minimum viable population, modelling, population dynamics, population viability analysis, South America, synergies

Software tools for conservation biologists

8 04 2013

Given 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.

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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 »

Comments : 23 Comments »
Tags: ARC/GIS, C#, Geographic information system, GIS, MAGICC/SCENGEN, MARK, Marxan, meta-model manager, Outbreak, population viability analysis, Python, R, RAMAS, Vortex, WINBUGS
Categories : climate change, conservation, conservation biology, disease, extinction, genetics, management, mathematics, metapopulation, minimum viable population, population dynamics, population viability analysis, protected area, PVA, research, reserve, software

Want to work with us?

22 03 2013

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

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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 »

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Tags: Australia, Australian Research Council, climate change, disease, ecology, Environmental science, epidemiology, extinction, invasive species, jobs, palaeo-ecology, positions, Postdoctoral Fellow, Research associate, species distribution models, University of Adelaide
Categories : alien species, Australia, biodiversity, climate change, conservation, conservation biology, demography, disease, environmental science, extinction, harvest, invasive species, population dynamics, population viability analysis, PVA, science, scientific writing, stochasticity, synergies, The University of Adelaide, threatened species

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!

Comments : 5 Comments »
Tags: Australia, cartoon, Crikey, First Dog on the Moon, Journal of Animal Ecology, population viability analysis, Thylacine, University of Adelaide
Categories : Australia, conservation, decline, disease, extinction, extinction vortex, habitat loss, harvest, kangaroo, population dynamics, population viability analysis, PVA

Translocations: the genetic rescue paradox

14 01 2013

Harvesting and habitat alteration reduce many populations to just a few individuals, and then often extinction. A widely recommended conservation action is to supplement those populations with new individuals translocated from other regions. However, crossing local and foreign genes can worsen the prospects of recovery.

We are all hybrids or combinations of other people, experiences and things. Let’s think of teams (e.g., engineers, athletes, mushroom collectors). In team work, isolation from other team members might limit the appearance of innovative ideas, but the arrival of new (conflictive) individuals might in fact destroy group dynamics altogether. Chromosomes work much like this – too little or too much genetic variability among parents can break down the fitness of their descendants. These pernicious effects are known as ‘inbreeding depression‘ when they result from reproduction among related individuals, and ‘outbreeding depression‘ when parents are too genetically distant.

Location of the two USA sites providing spawners of largemouth bass for the experiments by Goldberg et al. (3): the Kaskaskia River (Mississipi Basin, Illinois) and the Big Cedar Lake (Great Lakes Basin, Wisconsin). Next to the map is shown an array of three of the 72-litre aquaria in an indoor environment under constant ambient temperature (25 ◦C), humidity (60%), and photoperiod (alternate 12 hours of light and darkness). Photo courtesy of T. Goldberg.

Recent studies have revised outbreeding depression in a variety of plants, invertebrates and vertebrates (1, 2). An example is Tony Goldberg’s experiments on largemouth bass (Micropterus salmoides), a freshwater fish native to North America. Since the 1990s, the USA populations have been hit by disease from a Ranavirus. Goldberg et al. (3) sampled healthy individuals from two freshwater bodies: the Mississipi River and the Great Lakes, and created two genetic lineages by having both populations isolated and reproducing in experimental ponds. Then, they inoculated the Ranavirus in a group of parents from each freshwater basin (generation P), and in the first (G1) and second (G2) generations of hybrids crossed from both basins. After 3 weeks in experimental aquaria, the proportion of survivors declined to nearly 30% in G2, and exceeded 80% in G1 and P. Clearly, crossing of different genetic lineages increased the susceptibility of this species to a pathogen, and the impact was most deleterious in G2. This investigation indicates that translocation of foreign individuals into a self-reproducing population can not only import diseases, but also weaken its descendants’ resistance to future epidemics.

A mechanism causing outbreeding depression occurs when hybridisation alters a gene that is only functional in combination with other genes. Immune systems are often regulated by these complexes of co-adapted genes (‘supergenes’) and their disruption is a potential candidate for the outbreeding depression reported by Goldberg et al. (3). Along with accentuating susceptibility to disease, outbreeding depression in animals and plants can cause a variety of deleterious effects such as dwarfism, low fertility, or shortened life span. Dick Frankham (one of our collaborators) has quantified that the probability of outbreeding depression increases when mixing takes place between (i) different species, (ii) conspecifics adapted to different habitats, (iii) conspecifics with fixed chromosomal differences, and (iv) populations free of genetic flow with other populations for more than 500 years (2).

A striking example supporting (some of) those criteria is the pink salmon (Oncorhynchus gorbuscha) from Auke Creek near Juneau (Alaska). The adults migrate from the Pacific to their native river where they spawn two years after birth, with the particularity that there are two strict broodlines that spawn in either even or odd year – that is, the same species in the same river, but with a lack of genetic flow between populations. In vitro mixture of the two broodlines and later release of hybrids in the wild have shown that the second generation of hybrids had nearly 50% higher mortality rates (i.e., failure to return to spawn following release) when born from crossings of parents from different broodlines than when broodlines were not mixed (4).

Read the rest of this entry »

Comments : 4 Comments »
Tags: assisted colonisation, assisted dispersal, conservation, extinction, genetic rescue, heterosis, hybrid vigour, inbreeding, inbreeding depression, intervention, outbreeding, outbreeding depression, Ranavirus, Richard Frankham, supergenes, Tony Goldberg, translocations
Categories : Allee effect, connectivity, conservation, disease, extinction, fish, genetic diversity, genetics, inbreeding depression, introgression, management, metapopulation, minimum viable population, threatened species

The biggest go first

11 12 2012

The saying “it isn’t rocket science” is a common cliché in English to state, rather sarcastically, that something isn’t that difficult (with the implication that the person complaining about it, well, shouldn’t). But I really think we should change the saying to “it isn’t ecology”, for ecology is perhaps one of the most complex disciplines in science (whereas rocket science is just ‘complicated’). One of our main goals is to predict how ecosystems will respond to change, yet what we’re trying to simplify when predicting is the interactions of millions of species and individuals, all responding to each other and to their outside environment. It becomes quickly evident that we’re dealing with a system of chaos. Rocket science is following recipes in comparison.

Because of this complexity, ecology is a discipline plagued by a lack of generalities. Few, if any, ecological laws exist. However, we do have an abundance of rules of thumb that mostly apply in most systems. I’ve written about a few of them here on ConservationBytes.com, such as the effect of habitat patch size on species diversity, the importance of predators for maintaining ecosystem stability, and that low genetic diversity doesn’t exactly help your chances of persisting. Another big one is, of course, that in an era of rapid change, big things tend to (but not always – there’s that lovely complexity again) drop off the perch before smaller things do.

The prevailing wisdom is that big species have slower life history rates (reproduction, age at first breeding, growth, etc.), and so cannot replace themselves fast enough when the pace of their environment’s change is too high. Small, rapidly reproducing species, on the other hand, can compensate for higher mortality rates and hold on (better) through the disturbance. Read the rest of this entry »

Comments : 5 Comments »
Tags: Amazon, biodiversity, ecology, extinction, forests, William Laurance
Categories : alien species, Australia, biodiversity, climate change, conservation, decline, deforestation, disease, ecology, ecosystem function, exploitation, extinction, fisheries, fragmentation, genetic diversity, genetics, habitat loss, harvest, logging, rain forests, synergies

Toothed conflict

1 11 2012

Left: An Anatolian shepherd (a Turkish breed improved in the USA) guiding a herd of boer goats whose flesh is much appreciated by people in Namibia and South Africa. Right: A cheetah carrying a radio-transmitter, within a project assessing range movements of this feline for the Cheetah Conservation Fund. Cheetahs refrain from moving close to the herds when the latter are looked after by the guardian dogs. Photos courtesy of Laurie Marker.

Another corker from Salva. He’s chosen a topic this week that’s near and dear to my brain – the conservation of higher-order predators. As ConBytes readers will know, we’ve talked a lot about human-predator conflict and the inevitable losers in that battle – the (non-human) predators. From dingos to sharks, predator xenophobia is just another way we weaken ecosystems and ultimately harm ourselves.

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Rural areas devoted to livestock are part of the natural landscape, so it is inevitable (as well as natural) that predators, livestock and humans interact in such a mosaic of bordering habitats. However, their coexistence remains an unresolved conservation problem.

When two species, people, political parties, enterprises… want the same thing, they either share it (if possible) or one side eliminates the competitor. The fact that proteins are part of the diet of humans and other carnivore species has resulted in a trophic drama that goes back millennia. Nowadays, predators like eagles, coyotes, lions, wolves and raccoons are credited for attacks on cattle and poultry (and people!) in all continents. This global problem is not only economic, but interlaces culture, emotion, policy and sanitation (1-4). For instance, some carnivores are reservoirs of cattle diseases and contribute to pathogen dispersal (5, 6).

Management options

Managers of natural resources have implemented three strategies to handle these sorts of issues for livestock breeders in general (7). Those strategies can be complementary or exclusive on a case-by-case basis, and are chosen following cost-benefit assessments and depending on the conservation status of the predator species involved. (i) ‘Eradication’ aims to eliminate the predator, which is regarded as noxious and worthless. (ii) ‘Regulation’ allows controlled takes under quota schemes, normally for pre-defined locations, dates and killing methods. ‘Preservation’ is applied in protected areas and/or for rare or endangered species, and often requires monitoring and measures set to prevent illegal harvest or trade. Additionally, many livestock breeders receive money to compensate losses to predators (8).

Many experts now advocate non-lethal (preventive) measures that modify the behaviour of people, livestock or predators (2, 7). The use of livestock-guarding dogs is one of those preventive measures (9). As an example, Laurie Marker (director of the Cheetah Conservation Fund) et al. (10) studied the use of 117 Anatolian shepherds adopted by Namibian rangers between 1995 and 2002 (Fig. 1). In this African country, cheetahs (Acinonyx jubatus) selectively forage on small-sized cattle and juveniles. Despite this feline being protected nationally, Namibian laws authorise rangers to shoot cheetahs in situations of risk to people and their properties, with more than 6,000 cheetahs having been killed in the 1980s alone (11). Through face-to-face interviews, Marker found that since the arrival of the Anatolian shepherds, > 70 % of the rangers perceived a pronounced reduction in cattle mortality (10). Although, the use of livestock-guarding dogs has worked out fine in many places worldwide, it is no panacea. In many other instances, the dogs dissuade some predator species and not others from harassing the livestock, or are only effective in combination with other measures (7, 9). Read the rest of this entry »

Comments : 3 Comments »
Tags: Acinonyx, farming, human-wildlife conflict, livestock, mesopredator release, Namibia, Predation, ranchers, trophic cascades
Categories : Africa, agriculture, conservation, disease, economics, ecosystem function, environmental policy, harvest, livestock, management, predator, trophic cascades

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.

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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 »

Comments : Leave a Comment »
Tags: Adelaide, biodiversity, climate change, Doctor of Philosophy, extinction, invasion biology, invasive species, Paleontology, PhD, rabbit, scholarship, The University of Adelaide, turtle, university
Categories : alien species, Australia, conservation, conservation biology, disease, environmental science, health, invasive species, kangaroo, mathematics, niche model, population dynamics, science, South Australia, The University of Adelaide

Threats to biodiversity insurance from protected areas

26 07 2012

A red-eyed tree frog (Agalychnis callidryas) from Barro Colorado Island in Panama. This small island, just 1500 ha (3700 acres) in area, is one of the tropical protected areas evaluated in this study (photo © Christian Ziegler <zieglerphoto@yahoo.co>, Smithsonian Tropical Research Institute). Note: It is prohibited for any third party or agency to use or license this image; any use other then described above shall be subject to usage fees as determined solely by the photographer.

Much of conservation science boils down to good decision making: when, where and how we ‘set aside’ terrestrial or marine areas for specific protection against the ravages of human endeavour. This is the basis for the entire sub-discipline of conservation planning and prioritisation, and features prominantly in most aspects of applied conservation and restoration.

In other words, we do all this science to determine where we should emplace protected areas, lobby for getting more land and sea set aside so that we have ‘representative’ amounts (i.e., to prevent extinctions), and argue over the best way to manage these areas once established.

But what if this pinnacle of conservation achievement is itself under threat? What if many of our protected areas are struggling to insure biodiversity against human consumption? Well, it’d be a scary prospect, to say the least.

Think of it this way. We buy insurance policies to buffer our investments against tragedy; this applies to everything from our houses, worldly possessions, cars, livestock, health, to forest carbon stores. We buy the policies to give us peace of mind that in the event of a disaster, we’ll be bailed out of the mess with a much-needed cash injection. But what if following the disaster we learn that the policy is no good? What if there isn’t enough pay-out to fix the mess?

In biodiversity conservation, our ‘insurance’ is largely provided by protected areas. We believe that come what may, at least in these (relatively) rare places, biodiversity will persist despite our relentless consumerism.

Unfortunately, what we believe isn’t necessarily true.

Today I’m both proud and alarmed to present our latest research on the performance of tropical protected areas around the world. Published online in Nature this morning (evening, for you Europeans) is the 216-author (yes, that is correct – 216 of us) paper entitled “Averting biodiversity collapse in tropical forest protected areas” led by Bill Laurance. Read the rest of this entry »

Comments : 20 Comments »
Tags: biodiversity, conservation, environment, Kakadu National Park, national parks, Protected area, threats, tropics, William Laurance
Categories : Africa, alien species, Amazon, amphibian, Asia, biodiversity, conservation, conservation biology, decline, deforestation, disease, environmental policy, fire, fragmentation, governance, habitat loss, harvest, human overpopulation, invasive species, logging, monitoring, predator, protected area, rain forests, reserve, South America

Government pulls plug on Asian honeybee eradication

3 03 2011

Here’s another one from the bee man, Tobias Smith (PhD candidate at the University of Queensland). Tobias recently blogged about bee basics here on ConservationBytes.com (something I highly recommend for anyone interested on brushing up on bee facts and dispelling a few myths), so I asked him to follow up with this very important piece on the future of pollination in Australia. It concerns a nasty little invader recently dubbed the “flying cane toad” (not my analogy).

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http://www.flickr.com/photos/angela-and-andrew/1196369580/in/faves-lornet/

Over the last few weeks there has been much media attention given to the Asian honeybee (Apis cerana) incursion in far north Queensland. The Asian honeybee was first detected near Cairns in May 2007. Since then an effort to eradicate the bee has been made. This peaked during 2010, when over 40 bee eradication personnel were employed to hunt and destroy in areas around Cairns, the Atherton Tablelands, and other nearby locations.

In late January this year, the committee established to manage the eradication program (governments and industry), decided to pull the plug on eradication efforts (on money to pay for efforts that is). They decided it was no longer possible to achieve eradication (a majority decision, not a unanimous decision). The position to stop resources for eradication is not supported by industry, or ecological commentators. Arguments have been made that this is the only window of opportunity for eradication (for ever!), and that more resources need to be put towards it now, while there is still a chance of success.

A few points to be made about the Asian honeybee in Australia: Read the rest of this entry »

Comments : 3 Comments »
Tags: Apis cerana, bee, honeybee, invasive species, Joe Ludwig, pollination, Tim Low, Tobias Smith
Categories : alien species, biodiversity, conservation, disease, ecosystem function, ecosystem services, invasive species, pollination

More to bees than queens and honey

11 02 2011

Another great guest post, this time from Tobias Smith, a PhD candidate at the University of Queensland’s School of Biological Sciences. Tobias is investigating bee community shifts across a fragmented tropical landscape in far north Queensland, aiming to identify landscape variation in community composition of two important rainforest pollinator groups, bees and flies. I met Tobias a few years ago as part of the Thiaki rainforest reforestation project for which he is doing baseline surveys of bees and flies.

I asked him a while ago to write a ‘primer’ on bees for ConservationBytes.com since so many people really don’t much about the taxon (I include myself in that group). He’s done a brilliant job – everything you wanted to know about bees but were afraid to ask (in 1000 words).

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The frequently reported, gloomy news about bee declines is hard not to notice. Bees are in dire trouble around the world, and this trend has worrying implications for both ecosystems and human food production. As a result, popular media often reports on the plight of bees, regularly reciting the figure of one in three mouthfuls of food being dependent on the work of bees. While bees certainly are in major trouble, it can be easy to misinterpret statements often made in these kind of articles without a little general bee knowledge. So here are a few bee facts that, at the very least, we ecological representatives should be familiar with. This information should help give some perspective when interpreting bee news, and when engaging in exciting bee conversations at the shops.

There are approximately 20,000 bees species globally. Yet when most people think of bees they think of a single species, Apis mellifera, the western honey bee (introduced in most of its range, and also referred to as the European honeybee). This bee is certainly an important bee. It is managed as the usual pollinator of crops requiring biotic pollination, and it makes the honey we usually eat here in the developed world. Some say our domestication of this bee has been an important contributing factor in achieving the level of development that we humans have. There are however, about 19,999 other bee species out there, and most of them are very different to the western honeybee. Read the rest of this entry »

Comments : 10 Comments »
Tags: Apis, bee, Colony collapse disorder, Honey bee, Varroa
Categories : Asia, Australia, biodiversity, conservation, disease, ecosystem services, food, pollination, reforestation

Global erosion of ecosystem services

14 09 2010

A few months ago I was asked to give a lecture about erosion of ecosystem services to students in the University of Adelaide‘s Issues in Sustainable Environments unit. I gave that lecture last week and just uploaded a slidecast of the presentation (with audio) today.

I’ve reproduced the lecture here for your viewing pleasure. I hope you find the 45-minute presentation useful. Note that the first few minutes cover me referring to the Biodiversity film short that I posted not too long ago.

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CJA Bradshaw

Comments : 2 Comments »
Tags: ecosystem services, Education, environment, University of Adelaide, webinar
Categories : anthropocene, Australia, biodiversity, carbon, climate change, coasts, coral reefs, deforestation, disease, ecosystem services, environmental policy, extinction, fire, fisheries, flood, fragmentation, governance, habitat loss, harvest, health, human overpopulation, illegal fishing, kelp, logging, marine protected area, MPA, pollination, predator, protected area, Red List, seagrass, shark, The University of Adelaide, threatened species, water

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 Lacy, Prof 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 Fordham, Dr 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

Comments : 1 Comment »
Tags: Barry Brook, Bob Lacy, Chicago, ecological modelling, RAMAS, Resit Akcakaya, software, travel, Vortex
Categories : climate change, connectivity, conservation biology, disease, mathematics, metapopulation, modelling, niche model, population dynamics, population viability analysis, PVA, USA

Global pollinator declines

11 03 2010

Mention anything about ecosystem services – those ecological functions arising from the interactions between species that provide some benefit (source of food/clean water, health, etc.) to humanity¹ – and one of the most cited examples is pollination.

It’s really a no-brainer, hence its popularity as an example. Pollinators (mainly insects, but birds, bats and other assorted species too) don’t exist to pollinate plants; rather, their principal source of food acquisition happens to spread around the gametes of the plants they regularly visit. Evolution has favoured the dependence of species in such ways because the mutualism benefits all involved, and in some cases, this dependence has become obligate. So when the habitats that pollinators need to survive are reduced or destroyed, inevitably their population sizes decline and the plants on which they feed lose their main sources of gene-spreading.

So what? Well, about 80 % of all wild plant species require insect pollinators for fruit and seed set, and about 75 % of all human crops require pollination by insects (mostly bees). So it’s pretty frightening to consider that although our global population is at 6.8 billion and growing rapidly, our main food pollinators (bees) are declining globally (see also previous post on bee declines). Indeed, domestic honey bee stocks have declined in the USA by 59 % since 1947 and in Europe by 25 % since 1985. Scared yet?

Another thing people don’t tend to get is that a bee cannot live on rapeseed alone. Most pollinators require intact forests to complete many of their other life history requirements (breeding, shelter, etc.) and merely forage occasionally in crop lands. Cut down all the adjacent bush, and your crops will suffer accordingly.

These, and other titbits to keep you awake at night and worry about what your grandchildren might eat are highlighted in a recent review in Trends in Ecology and Evolution by Potts and colleagues entitled Global pollinator declines: trends, impacts and drivers.

What’s driving all this loss? Several things, but it’s mainly due to ‘land-use change’ (a bullshit word people use generally to mean habitat loss, fragmentation and degradation). However, invasive species competition, pathogens and parasites, and climate change (and the synergies amongst all of these) are all contributing.

It always amazes me when people ask me why biodiversity is important. Despite the overwhelming knowledge we’ve accumulated about how functioning ecosystems make the planet liveable, despite it just being plainly stupid to think that humans are somehow removed from normal biological processes, and even with such in-your-face examples of global pollinator declines and the real, extremely worrying implication for food supplies, many people just don’t seem to get it. Every tree you cut down, every molecule of carbon dioxide you release, every drop of water you waste will punish you and your family directly for generations to come. How much more self-evident can you get?

Humanity seems to have a very poorly developed sense of self-preservation.

CJA Bradshaw

¹It’s amazingly arrogant and anthropocentric to think of anything in ecosystems as ‘providing benefits to humanity’. After all, we’re just another species in a complex array of species within ecosystems – we just happen to be one of the numerically dominant ones, excel at ecosystem ‘engineering’ and as far as we know, are the only (semi-) sentient of the biologicals. Although the concept of ecosystem services is, I think, an essential abstraction to place emphasis on the importance of biodiversity conservation to the biodiversity ignorant, it does rub me a little the wrong way. It’s almost ascribing some sort of illogical religious perspective that the Earth was placed in its current form for our eventual benefit. We might be a fairly new species in geological time scales, but don’t think of ecosystems as mere provisions for our well-being.

Potts, S., Biesmeijer, J., Kremen, C., Neumann, P., Schweiger, O., & Kunin, W. (2010). Global pollinator declines: trends, impacts and drivers Trends in Ecology & Evolution DOI: 10.1016/j.tree.2010.01.007

Comments : 18 Comments »
Tags: bees, biodiversity, conservation, ecosystem services, pollination, pollinator, science
Categories : agriculture, alien species, biodiversity, climate change, conservation, decline, deforestation, disease, ecosystem function, ecosystem services, habitat loss, invasive species, pollination

Sick environment, sick people

30 10 2009

A quick post to talk about a subject I’m more and more interested in – the direct link between environmental degradation (including biodiversity loss) and human health.

To many conservationists, people are the problem, and so they focus naturally on trying to maintain biodiversity in spite of human development and spread. Well, it’s 60+ years since we’ve been doing ‘conservation biology’ and biodiversity hasn’t been this badly off since the Cretaceous mass extinction event 146-64 million years ago. We now sit squarely within the geological era more and more commonly known as the ‘Anthropocene’, so if we don’t consider people as an integral part of any ecosystem, then we are guaranteed to fail biodiversity.

I haven’t posted in a week because I was in Shanghai attending the rather clumsily entitled “Thematic Reference Group (TRG) on Environment, Agriculture and Infectious Disease’, which is a part of the UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR) (what a mouthful that is). What’s this all about and why is a conservation ecologist (i.e., me) taking part in the group?

It’s taken humanity a while to realise that what we do to the planet, we eventually end up doing to ourselves. The concept of ecosystem services¹ demonstrates this rather well – our food, weather, wealth and well-being are all derived from healthy, functioning ecosystems. When we start to bugger up the inter-species relationships that define one element of an ecosystem, then we hurt ourselves. I’ve blogged about this topic a few times before with respect to flooding, pollination, disease emergence and carbon sequestration.

Our specific task though on the TRG is to define the links between environmental degradation, agriculture, poverty and infectious disease in humans. Turns out, there are quite a few examples of how we’re rapidly making ourselves more susceptible to killer infectious diseases simply by our modification of the landscape and seascape.

Some examples are required to illustrate the point. Schistosomiasis is a snail-borne fluke that infects millions worldwide, and it is on the rise again from expanding habitat of its host due to poor agricultural practices, bad hygiene, damming of large river systems and climate warming. Malaria too is on the rise, with greater and greater risk in the endemic areas of its mosquito hosts. Chagas (a triatomine bug-borne trypanosome) is also increasing in extent and risk. Some work I’m currently doing under the auspices of the TRG is also showing some rather frightening correlations between the degree of environmental degradation within a country and the incidence of infectious disease (e.g., HIV, malaria, TB), non-infectious disease (e.g., cancer, cardiovascular disease) and indices of life expectancy and child mortality.

I won’t bore you with more details of the group because we are still drafting a major World Health Organization report on the issues and research priorities. Suffice it to say that if we want to convince policy makers that resilient functioning ecosystems with healthy biodiversity are worth saving, we have to show them the link to infectious disease in humans, and how this perpetuates poverty, rights injustices, gender imbalances and ultimately, major conflicts. An absolute pragmatist would say that the value of keeping ecosystems intact for this reason alone makes good economic sense (treating disease is expensive, to say the least). A humanitarian would argue that saving human lives by keeping our ecosystems intact is a moral obligation. As a conservation biologist, I argue that biodiversity, human well-being and economies will all benefit if we get this right. But of course, we have a lot of work to do.

CJA Bradshaw

¹Although Bruce Wilcox (another of the TRG expert members), who I will be highlighting soon as a Conservation Scholar, challenges the notion of ecosystem services as a tradeable commodity and ‘service’ as defined. More on that topic soon.