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.

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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 »


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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

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 Codfish, Anchor 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.

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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 »


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Categories : Allee effect, captive breeding, conservation, decline, extinction, fragmentation, invasive species, kakapo, management, New Zealand, population dynamics, Red List, threatened species

Brave new green world: biodiversity’s response to Australia’s carbon economy

12 03 2013

carbon farming 2I’ve had a busy weekend entertaining visiting colleagues and participating in WOMADelaide‘s first-ever ‘The Planet Talks‘. If you haven’t heard of WOMADelaide, you’re truly missing out in one of the best music festivals going (and this is from a decidedly non-festival-going sort). Planet Talks this year was a bit of an experiment after the only partially successful Earth Station festival held last year (it was well-attended, but apparently wasn’t as financially successful as they had hoped). So this year they mixed a bit of science with a bit of music – hence ‘Planet Talks’. Paul Ehrlich was one of the star attractions, and I had the honour of going onstage with him yesterday to discuss a little bit about human population growth and sustainability. It was also great to see Robyn Williams again. All the Talks were packed out – indeed, I was surprised they were so popular, especially in the 39-degree heat. Rob Brookman, WOMADelaide’s founder and principal organiser, told me afterward that they’d definitely be doing it again.

But my post really isn’t about WOMADelaide or The Planet Talks (even though I got the bonus of meeting one of my favourite latin bands, Novalima, creators of one of my favourite songs). It’s instead about a paper I heralded last year that’s finally been accepted.

In early 2012 at the Terrestrial Ecosystem Research Network (TERN) symposium in Adelaide, the Australian Centre for Ecological Analysis and Synthesis (ACEAS) put on what they called the ‘Grand Challenges’ workshop. I really didn’t get the joke at the time, but apparently the ‘grand challenge’ was locking 30 scientists with completely different backgrounds in a room for two days to see if they could do anything other than argue and bullshit. Well, we rose to that challenge and produced something that I think is rather useful.

I therefore proudly introduce the paper entitled Brave new green world: consequences of a carbon economy for the conservation of Australian biodiversity just accepted in Biological Conservation. The online version isn’t quite ready yet (should be in the next few weeks), but you are welcome to request a preprint from me now. If you attended (the surprisingly excellent) TERN symposium in Canberra last month, you might have seen me give a brief synopsis of our results.

The paper is a rather  in-depth review of how we, 30 fire, animal, plant, soil, landscape, agricultural and freshwater biologists, believe Australia’s new carbon-influenced economy (i.e., carbon price) will impact the country’s biodiversity. Read the rest of this entry »


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Categories : agriculture, Australia, biocarbon, biodiversity, biosequestration, carbon, carbon trading, climate change, climate shift, conservation, conservation biology, deforestation, ecology, economics, ecosystem function, environmental economics, environmental policy, fire, fragmentation, habitat loss, harvest, invasive species, kangaroo, livestock, logging, management, monitoring, planning, recovery, reforestation, restoration, southern Australia, synergies, water

Translocations: the genetic rescue paradox

14 01 2013

helphindranceHarvesting 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.

CB_OutbreedingDepression Photo
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 »


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Categories : Allee effect, connectivity, conservation, disease, extinction, fish, genetic diversity, genetics, inbreeding depression, introgression, management, metapopulation, minimum viable population, threatened species

Protected areas work, but only when you put in the effort

15 11 2012

Apologies for the delay in getting this latest post out. If you read my last one, you’ll know that I’ve been in the United Kingdom for the last week. I’m writing this entry in the train down from York to Heathrow, from which I’ll shortly begin the gruelling 30-hour trip home to Adelaide.

Eight days on the other side of the planet is a bit of a cyclonic trip, but I can honestly say that it was entirely worth it. My first port of call was London where I attended the Zoological Society of London’s Protected Areas Symposium, which is the main topic on which I’ll elaborate shortly.

But I also visited my friend and colleague, Dr. Kate Parr at the University of Liverpool, where I also had the pleasure of talking with Rob Marrs and Mike Begon. Liverpool was also where I first observed the habits of a peculiar, yet extremely common species – the greater flabby, orange-skinned, mini-skirted, black-eyed scouser. Fascinating.

I then had the privilege and serendipitous indulgence of visiting the beautiful and quaint city of York where I gave another talk to the Environment Department at the University of York. My host, Dr. Kate Arnold was simply lovely, and I got to speak with a host of other very clever people including Callum Roberts, Phil Platts, Andy Marshall and Murray Rudd. Between the chats and real ales, mushy peas, pork pies and visits to the Minster, I was in north English heaven.

Enough of the cultural compliments – the title of this post was the take-home message of the ZSL symposium. There I gave a 25-minute talk summarising our recent paper on the performance of tropical protected areas around the globe, and added a few extra analyses in the process. One interesting result that was missing from the original paper was the country-level characteristics that explain variation in protected area ‘health’ (as we defined it in the Nature paper). After looking at a number of potential drives, including per-capita wealth, governance quality, environmental performance, human population density and the proportion of high conservation-value protected areas (IUCN Ia, Ib, II and IV categories), it came out that at least at that coarse country scale that only the proportion of high conservation-value protected areas explained any additional variation in health. In other words, the more category Ia, Ib, II and IV protected areas a country has (relative to the total), the better their protected areas do on average (and remember, we’re talking largely about developing and tropical nations here). Read the rest of this entry »


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Categories : biodiversity, conference, conservation, decline, deforestation, environmental policy, extinction, governance, habitat loss, harvest, logging, management, planning, protected area, tropical

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 »


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Categories : Africa, agriculture, conservation, disease, economics, ecosystem function, environmental policy, harvest, livestock, management, predator, trophic cascades

Tropical protected areas still in trouble

8 10 2012

© P. Harris

There’s nothing like a bit of good, intelligent and respectful debate in science.

After the publication in Nature of our paper on tropical protected areas (Averting biodiversity collapse in tropical forest protected areas), some interesting discussion has ensued regarding some of our assumptions and validations.

As is their wont, Nature declined to publish these comments (and our responses) in the journal itself, but the new commenting feature at Nature.com allowed the exchange to be published online with the paper. Cognisant that probably few people will read this exchange, Bill Laurance and I decided to reproduce them here in full for your intellectual pleasure. Any further comments? We’d be keen to hear them.

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COMMENT #1 (by Hari Sridhar of the Centre for Ecological Sciences at the Indian Institute of Science in Bangalore)

In this paper, Laurance and co-authors have tapped the expert opinions of ‘veteran field biologists and environmental scientists’ to understand the health of protected areas in the tropics worldwide. This is a novel and interesting approach and the dataset they have gathered is very impressive. Given that expert opinion can be subject to all kinds of biases and errors, it is crucial to demonstrate that expert opinion matches empirical reality. While the authors have tried to do this by comparing their results with empirical time-series datasets, I argue that their comparison does not serve the purpose of an independent validation.

Using 59 available time-series datasets from 37 sources (journal papers, books, reports etc.), the authors find a fairly good match between expert opinion and empirical data (in 51/59 cases, expert opinion matched empirically-derived trend). For this comparison to serve as an independent validation, it is crucial that the experts were unaware of the empirical trends at the time of the interviews. However, this is unlikely to be true because, in most cases, the experts themselves were involved in the collection of the time-series datasets (at least 43/59 to my knowledge, from a scan of references in Supplementary Table 1). In other words, the same experts whose opinions were being validated were involved in collection of the data used for validation.

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OUR RESPONSE (William F. Laurance, Corey J. A. Bradshaw, Susan G. Laurance)

Sridhar raises a relevant point but one that, on careful examination, does not weaken our validation analysis. Read the rest of this entry »


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Categories : biodiversity, bushmeat, conservation, decline, deforestation, environmental policy, exploitation, extinction, fragmentation, governance, habitat loss, harvest, invasive species, logging, management, protected area, rain forests, science, South America, South East Asia, threatened species

No-extinction targets are destined to fail

21 09 2012

I’ve been meaning to write about this for a while, and now finally I have been given the opportunity to put my ideas ‘down on paper’ (seems like a bit of an old-fashioned expression these days). Now this post might strike some as overly parochial because it concerns the state in which I live, but the concept applies to every jurisdiction that passes laws designed to protect biodiversity. So please look beyond my navel and place the example within your own specific context.

As CB readers will appreciate, I am firmly in support of the application of conservation triage – that is, the intelligent, objective and realistic way of attributing finite resources to minimise extinctions for the greatest number of (‘important’) species. Note that deciding which species are ‘important’ is the only fly in the unguent here, with ‘importance’ being defined inter alia as having a large range (to encompass many other species simultaneously), having an important ecological function or ecosystem service, representing rare genotypes, or being iconic (such that people become interested in investing to offset extinction.

But without getting into the specifics of triage per se, a related issue is how we set environmental policy targets. While it’s a lovely, utopian pipe dream that somehow our consumptive 7-billion-and-growing human population will somehow retract its massive ecological footprint and be able to save all species from extinction, we all know that this is irrevocably  fantastical.

So when legislation is passed that is clearly unattainable, why do we accept it as realistic? My case in point is South Australia’s ‘No Species Loss Strategy‘ (you can download the entire 7.3 Mb document here) that aims to

“…lose no more species in South Australia, whether they be on land, in rivers, creeks, lakes and estuaries or in the sea.”

When I first learned of the Strategy, I instantly thought to myself that while the aims are laudable, and many of the actions proposed are good ones, the entire policy is rendered toothless by the small issue of being impossible. Read the rest of this entry »


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Categories : Australia, biodiversity, conservation, conservation biology, deforestation, ecosystem function, ecosystem services, environmental policy, extinction, extinction debt, function, genetic diversity, habitat loss, human overpopulation, management, monitoring, planning, prioritisation, reforestation, South Australia

Native invaders divide loyalties

7 09 2012

California sea lion at Bonneville fish ladder. Credit: U.S. National Oceanic and Atmospheric Administration

As if to mimic the weirder and weirder weather human-caused climate disruption is cooking up for us, related science stories seem to come in floods and droughts. Yes, research trends become fashionable too (imagine a science fashion show? – but I digress…).

Only yesterday, the ABC published an opinion piece on the controversies surrounding which species we call ‘native’ and ‘invasive’ (based on a recent paper published in Global Ecology and Biogeography), and in June this year, Salvador Herrando-Pérez wrote a great little article on the topic entitled “The invader’s double edge“.

Then today, I received a request to publish a guest post here on ConservationBytes.com from Lauren Kuehne, a research scientist in Julian Olden‘s lab at the University of Washington in Seattle. The topic? Why, the controversies surrounding invasive species, of course! Lauren’s following article demonstrates yet again that it’s not that simple.

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A drawback to the attention garnered by high-profile invasive species is the tendency to infer that every non-native species is bad news, the inverse assumption being that all native species must be ‘good’. While this storyline works well for Hollywood films and faerie tales, in ecology the truth is rarely that simple. A new review article in the September issue of Frontiers in Ecology and the Environment, describes the challenges and heartbreaks when native species run amok in the sense of having negative ecological impacts we typically associate with non-native species. Examples in the paper range from unchecked expansions of juniper trees in sagebrush ecosystems with wildfire suppression, to overgrazing by elk (wapiti) released from predation following the removal of wolves and mountain lions. Read the rest of this entry »


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Categories : alien species, climate change, conservation, fish, invasive species, management, threatened species, USA

Restoring doomed fish

24 08 2012

I get called a doomsday merchant a lot, mainly because there’s not a lot of good news out there when it comes to biodiversity these days. However, now and again there is a success story worth shouting from the rooftops. This latest post comes from my PhD student, Jarod Lyon (also of the Arthur Rylah Institute in Victoria), who is working on restoring native freshwater fish in Australia’s largest river system – the Murray-Darling. The M-D also happens to be in a lot of trouble because of poor water management and years of neglect. However, some clever research and restoration proves that we can bring biodiversity back from the brink if done right. Jarod has posted here on Conservation Bytes before describing his work, and this latest post provides some detail on one species in particular.

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Trout cod Maccullochella macquariensis were once considered to be widespread in the southern tributaries of the Murray-Darling Basin. However over the past fifty years, their distribution and abundance have declined dramatically, due to a number of disturbances including habitat loss, altered flow and temperature patterns, in-stream sedimentation, population fragmentation due to in-stream barriers and over fishing. Trout cod are listed nationally as endangered under the Environment Protection and Biodiversity Conservation Act (EPBC Act 1999) and listed under the Victorian Flora and Fauna Guarantee Act (FFG Act 1988). Trout cod are often accidentally caught when fishing for Murray cod. However, it is illegal to take a trout cod while angling.

Trout cod were historically abundant in the lower Ovens River system in South-Eastern Australia, however were locally extinct by the 1980s. In an attempt to re-introduce a viable population in the Ovens River, hatchery-reared juvenile trout cod were stocked in the Ovens River system for ten years starting in 1997. Our recent manuscript published in Marine and Freshwater Research assesses the success of this stocking regime (particularly in relation to recovery plan objectives) through a variety of techniques, including fish surveys and analysis of gonads, otoliths and genetic structure of the population.

We found that the Ovens River now holds a naturally self-sustaining population of trout cod – that is, the progeny of stocked fishes are now breeding.  Given that most threatened species re-introduction programs worldwide fail, this is somewhat of a good-news story for management of rare animals. In particular, we found that the length of the stocking program was a major factor in its success, as the long time period overcame the years where the survival of the stocked fingerlings was low. Interestingly, most fish to recruit to an adult size were stocked in 2003 or 2004 – meaning if this had been a five-year program, it would most likely have failed. Read the rest of this entry »


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Categories : Australia, conservation, decline, fish, fisheries, genetics, habitat loss, management, Murray cod, research, resnagging, restoration, River Murray, southern Australia, trout cod

Get boreal

7 06 2012

I’ve been a little quiet this last week because I’ve had to travel to the other side of the planet for what turned out to be a very interesting and scientifically lucrative workshop. After travelling 31 hours from Adelaide to Umeå in northern Sweden, I wondered to myself if it was going to be worth it for a 2.5-day workshop on a little island (Norrbyskär) in the Baltic Sea (which, as it turned out, didn’t have internet access).

The answer is a categorical ‘yes’!

Many of you know that I’ve dabbled in boreal forest conservation in the past, but I could never claim any real expertise in the area. Hence it came as something of a shock when Jon Moen of Umeå University asked me to attend a specialist workshop focused loosely on making the plight and importance of the boreal forest more widely acknowledged. I dragged my feet initially, but Jon convinced me that I could add something to the mix.

It was a small workshop, but well-represented by all boreal countries save Norway (i.e., we had Russians, Swedes, Finns, Canadians and Americans – this Australian was indeed the odd one out). We also had a wide array of expertise, from carbon accountants, political scientists, political economists, native cultures experts, ecologists to foresters. Our mandate – justify why we should pay more attention to this globally important region.

Just how important is the boreal forest? We managed to unearth some little-appreciated facts: Read the rest of this entry »


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Categories : Arctic, biocarbon, biodiversity, biosequestration, Canada, climate change, conservation, deforestation, economics, ecosystem, ecosystem services, environmental policy, Europe, habitat loss, harvest, logging, management, Norway, reforestation, Russia, Sweden, USA

Can Australia afford the dingo fence?

18 05 2012

I wrote this last night with Euan Ritchie of Deakin University in response to some pretty shoddy journalism that misrepresented my comments (and Euan’s work). Our article appeared first in The Conversation this morning (see original article).

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We feel we have to set the record straight after some of our (Bradshaw’s) comments were taken grossly out of context, or not considered at all (Ritchie’s). A bubbling kerfuffle in the media over the last week compels us to establish some facts about dingoes in Australia, and more importantly, about how we as a nation choose to manage them.

A small article in the News Ltd. Adelaide Advertiser appeared on 11 May in which one of us (Bradshaw) was quoted as advocating the removal of the dingo fence because it was not “cost effective” (sic). Despite nearly 20 minutes on the telephone explaining to the paper the complexities of feral animal management, the role of dingoes in suppressing feral predators, and the “costs” associated with biodiversity enhancement and feral control, there wasn’t a single mention of any of this background or justification.

Another News Ltd. article denouncing Ritchie’s work on the role of predators in Australian ecosystems appeared in The Weekly Times the day before, to which Ritchie responded in full.

So it’s damage control, and mainly because we want to state categorically that our opinion is ours alone, and not that of our respective universities, schools, institutes or even Biosecurity SA (which some have claimed or insinuated, falsely, that we represent). Biosecurity SA is responsible for, inter alia, the dingo fence in South Australia. Although our opinions differ on its role, we are deeply impressed, grateful and supportive of their work in defending us from biological problems. Read the rest of this entry »


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Categories : Australia, biodiversity, cat, conservation, dingo, ecosystem function, ecosystem services, environmental policy, extinction, fox, function, harvest, invasive species, livestock, mammal, management, predator, southern Australia, threatened species, trophic cascades

The wounded soldiers of biodiversity

10 04 2012

Here’s another great post from Salvador Herrando-Pérez. It is interesting that he’s chosen an example species that was once (a long, long time ago in a galaxy far, far away) of great interest to me (caribou – see ancient papers a, b, c, d). But that is another story. Take it away, Salva.

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–Figure 1. Caribou (reindeer) are ungulates weighing up to ~ 100 kg. They live in tundra and taiga in Finland, Greenland, Finland, Norway, Mongolia, Russia, Canada and USA (extinct in Sweden). The species is globally stable (‘Least Concern’, IUCN Red List), but the subspecies of woodland caribou (Rangifer tarandus caribou) is threatened in North America. Schneider and colleagues’ 7 study encompasses ~ 3,000 individuals in 12 herds (75 to 450 individuals per herd), occupying ~ 100.000 km2 of conifer forest and peatland (3,000 to 19,000 km2 per herd). Two ecotypes are recognized regionally22, namely migratory mountain herds (mostly from mountains and foothills in west-central Alberta), and non-migratory boreal herds (mostly from peatlands in central and northern Alberta). The photo shows a group of caribous grazing on subalpine vegetation from Tonquin Valley, Jasper National Park (Alberta, Canada). Photo courtesy of Saakje Hazenberg.–

As conservation biology keeps incorporating management and economical principles from other disciplines, it stumbles with paradoxes such that investing on the most threatened components of biodiversity might in turn jeopardize the entire assets of biodiversity.

At the end of 2011, newspapers and TVs echoed an IUCN report cataloguing as ‘extinct’ or ‘near extinct’ several subspecies of rhinos in Asia and Africa. To many, such news might have invoked the topic: “how badly governments do to protect the environment”. However if, to avoid those extinctions, politicians had to deviate funds from other activities, what thoughts would come to the mind of workers whose salaries had to be frozen, school directors whose classroom-roof leakages could not be repaired (e.g., last winter at my niece’s school in Spain), colonels whose last acquisition of ultramodern tanks had to be delayed, or our city council’s department who had to cancel Sting’s next performance.

Thus, there are three unquestionable facts regarding species conservation:

  1. the protection of species costs money;
  2. governments and environmental organisations have limited budgets for a range of activities they deem necessary; and
  3. our way of conserving nature is failing because, despite increasing public/private support and awareness, the rate of destruction of biodiversity is not decelerating1,2.

One of the modern debates among conservationists pivots around how to use resources efficiently3-6. Schneider and colleagues7 have dealt with this question for woodland caribou (Rangifer tarandus) in Canada. A total of 18 populations of this ungulate persist in the Canadian province of Alberta, all undergoing demographic declines due to mining extractions (oil, gas and bitumen), logging and wolf predation. The species is listed as ‘threatened’ regionally and nationally. The Alberta Caribou Recovery Plan (2004-2014) is attempting to protect all herds. Under such a framework, Schneider et al.7 predicted that woodland caribou would be regionally extirpated in less than a century.

Furthermore, they estimated the costs of making each herd viable (Fig. 1), with a triple revelation. To save all herds from extinction would need ~ CA$150,000 million (beyond the available budget). The most threatened herds are among the most expensive to protect (within present management approach). Some herds would be secured through modest investment for two decades. Overall, their study suggests that Alberta’s woodland caribou would be eligible for triage, i.e., at the subpopulation level8. Read the rest of this entry »


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Categories : boreal, Canada, climate change, conservation, deforestation, environmental policy, ethics, fire, fragmentation, habitat loss, harvest, logging, mammal, management, planning, recovery, reforestation, temperate

Give way to the invader

25 01 2012

By weird coincidence, Salvador Herrando-Pérez (student blogger extra-ordinaire – see his previous posts on evolution, pollination, bird losses, taxonomic inflation, niche conservatism, historical biogeography, ecological traps and ocean giants) has produced a post this week expanding on the problem of roads. Also weirdly coincidental is that both Salva and I are in his home country of Spain this week.

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Australia’s > 800,000-km road network would go 60 times around the equator of our planet. Confined to the boundaries of any one country, roads are a conspicuous component of the landscape, and shape the dispersion, survival and reproduction of many plants and animals in urban and remote areas.

Those who drive (or are driven by) will be familiar with the image of a crushed kangaroo on the roadside (a hedgehog in Europe), or the sticky mosaic of insects smashed against the windscreen after a high-speed run. Mortality by collision is one of the many effects that roads can have on the demography of organisms – including humans. Those effects encompass

  • physical alteration of terrestrial and aquatic habitats,
  • chemical pollution leakage during road construction and maintenance, and from asphalt compounds during storms,
  • alteration of animal behaviour (e.g., change in home range, or in patterns of flight or vocalisation),
  • access to remote areas by hunters, fishermen and gatherers in general, and
  • intense habitat fragmentation1-3.

However, some species get around those negative impacts by using the roads as pathways to new territories, thereby eluding barriers like seas, mountains, rivers, dense vegetation, or competition for vital resources with other species. Read the rest of this entry »


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Categories : alien species, Australia, conservation, demography, environmental engineering, environmental policy, evolution, fragmentation, invasive species, management, predator, temperate, tropical

Surgical conservation: gain requires some pain

21 12 2011

© 2008-2011 ~Hiuki http://fav.me/d1j3ns9

I apologise to CB readers for the unusually low frequency of posts this month. With the International Congress for Conservation Biology taking up a lot of my time earlier this month, and the standard palaver of xmas preparations (i.e., getting shit done before the end of the year), I’m afraid the blog has taken a back seat. Now officially ‘on leave’ (whatever that means for an academic), I have found a brief window during which I can put a few thoughts together.

For this post I must take you back to October 2011 when, if you were in Australia, you might have heard about the so-called ‘debacle‘ of the Macquarie Island rabbit/rate/mouse-eradication programme in which it was identified that a few thousand seabirds had become the collateral damage.

To recap, an intense poisoning programme was initiated on subantarctic Macquarie Island to eradicate these pests after years of massive environmental degradation had finally forced the government’s (of Tasmania and the Commonwealth) hand to do something. What caught my eye in all this was the sheer stupidity and politicking associated with the programme, in which hyper-conservative Eric Abetz (Liberal Senator for Tasmania) managed to turn this amazing success into a Labor-bashing political sledge-hammer.

Abetz is no stranger to anti-environmentalism and fights vehemently for Tasmania’s forest-raping industry; he considers political parties such as the Greens, environmental groups such as The Wilderness Society and pro-democracy groups such as Get Up! his mortal enemies. He’s even had a go at esteemed author Richard Flanagan for supporting the anti-deforestation movement in Tasmania! Read the rest of this entry »


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Categories : alien species, Australia, conservation, environmental policy, extinction, invasive species, management, research, science

Where are they? Finding (and conserving) the biggest fish in the sea

16 11 2011

A post from my PhD student, Ana Sequeira, on her latest paper just out in Diversity and Distributions: Ocean-scale prediction of whale shark distribution.

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© W Osborn (AIMS)

The ocean is our major source of water, it stabilises our breathable atmosphere and provides many supplies such as medicines (e.g., anti-cancer therapy drugs1) and food. Despite its the importance for human life, many marine species are now at a high risk of extinction owing to human changes to the oceans.

The whale shark (Rhincodon typus, Smith 1828) – an icon of the oceans of a spectacularly huge size and docile character – is just one of those species.

Despite being a fish that many people (mainly in Southeast Asia) are happy to have on their plate, whale sharks are worth millions of dollars every year in the ecotourism industry worldwide. One would then expect that being such a profitable species, their ecology would be well known and thoroughly studied.

The reality is quite different.

Basic information on whale sharks such as the whereabouts of their breeding areas, the average number of offspring per female, or even how many individuals still exist, is not currently known. Moreover, despite the genetic evidence that whale sharks worldwide are connected among different oceans, it is unclear if they move from places where they are protected to places where they are still illegally fished.

Information on distribution and patterns of occurrence in space and time is essential for conservation, and can help to save entire ecosystems if used correctly, for example: to isolate important mating and breeding areas.

To identify the whale shark’s seasonal distribution patterns in the Indian Ocean, to test if records follow a decreasing trend over time, and if occurrence is related to variation in climatic signals, we used multivariate distribution models of seasonal and inter-annual whale shark sightings opportunistically collected over 17 years by the tuna purse-seine fishery. Read the rest of this entry »


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Categories : Asia, Australia, conservation, fish, fisheries, harvest, illegal fishing, management, marine, protected area, shark, South East Asia, species distribution model, threatened species

Oceans need their giants

2 11 2011

Another great post from Salvador Herrando Pérez.

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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 »


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Categories : caviar, conservation, exploitation, fish, fisheries, harvest, management, marine, population dynamics

Crocodiles, spiders and leeches

11 04 2011

I just wrote a fun little piece for a new section in the journal Frontiers in Ecology and the Environment that they’re calling Trails and Tribulations. The basic idea is that the author recounts a particularly interesting field-related experience through which an ecological concept is woven.

Editor-in-Chief Sue Silver said that I could reproduce my article here as long as I acknowledged Frontiers and the Ecological Society of America. It was fun to write, and I hope you enjoy it too [the PDF of the article is available free of charge here].

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“So does each team get a hand gun?”

“No, you get an oar”

“What good is an oar?”

“Listen, mate. When a 3-metre croc jumps out of the swamp at you, there is nothing more natural in the world than to thump him with a big stick. It’s an autonomous response. With a gun, IF you manage to keep it dry, and IF you manage to get it out in time before the croc bites off your head, chances are you’ll just shoot the bloke in front of you anyway. So you get an oar.”

“Fair enough”.

That is an approximate, paraphrased reproduction of the initial conversation I had with renowned Australian crocodile biologist, Grahame Webb, just prior to my first (and as it turns out, only) trip to collect crocodile eggs for his Darwin wildlife park and crocodile farm. I volunteered to take part in the collection because I had recently begun working with Grahame and his team tracking the world’s largest crocodile species – the saltwater or estuarine crocodile Crocodylus porosus – and modelling aspects of its populations (Bradshaw et al. 2006). Having already been out on several occasions to harpoon and satellite-tag animals (some measuring > 4 m) on the Mary River, and cage-trap others in Kakadu National Park, I thought a little egg collection would be a proverbial walk in the park. Little did I know that it would end up being one of my more memorable experiences.

Let me walk you through the process. First, you wait until the height of the wet season and drive out as far as you can toward the breeding swamp of interest (in this case, Melacca Swamp in the Adelaide River flood plain, about one hour’s drive from Darwin). Then you and two other loonies pile into a small helicopter equipped with landing pontoons which ferries you to one of many previously identified crocodile nests. Because there is usually too much vegetation around the nest itself, the helicopter must land about 100-300 m away. Clothed only in long pants, a long-sleeved shirt and cotton gloves to protect your skin from the slicing blade grass, you jump off the helicopter’s pontoons into impenetrably murky, chest-deep water. One of the team drags an esky (chiller box into which eggs will be placed) and another carries an oar. As the noise of the departing helicopter becomes a faint buzz, you suddenly realise via the rapid expansion of your terminal sphincter that you are in the middle of a crocodile-filled swamp – and you are holding an oar. Read the rest of this entry »


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Categories : Australia, celebrity, conservation, conservation biology, environmental policy, exploitation, extinction, harvest, management, predator, research

Build a bridge out of ‘er

12 03 2011

Apologies to Monty Python and my poor attempt to make the over-used expression ‘bridging the gap’ humorous.

Today’s guest post comes from across the Pacific Ocean. Dr. Sara Maxwell is a postdoctoral fellow with Marine Conservation Biology Institute and University of California Santa Cruz, Long Marine Laboratory. She was kind enough to contribute to ConservationBytes.com about an issue I’ve covered before in various forms – making conservation research relevant for conservation action.

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© R. Arlettaz

In a catalyzing article titled “From publications to public actions: when conservation biologists bridge the gap between research and implementation” in the November 2010 issue of BioScience, Raphaël Arlettaz1 and his colleagues Michael Schaub2, Jérôme Fournier3, Thomas Reichlin2, Antoine Sierro4, James Watson5 and Veronika Braunisch2 explore reasons for our hard work as conservation biologists not reaching the implementation phase. This article strongly resonated with my colleague, Kiki Jenkins6 and I, Sara Maxwell. This resulted in a series of letters published in BioScience and now we join together, along with Jeffrey Camm7, Guillaume Chapron8, Liana Joseph9, and Rudi Suchant10 to synthesize our ideas and present them to the larger conservation community via ConservationBytes.

The article that sparked the discussion

In their article, Arlettaz and colleagues highlight some of the main roadblocks to implementing conservation research. The main reasons are that:

  1. The research made by conservation biologists’ does not lend itself well to implementation, i.e., as a community we often focus on the wrong questions or address them in ways that do not lead to practical applications for practitioners;
  2. The outcomes of conservation biologists’ research tends not to reach practitioners and so fails to be put into action;
  3. When we successfully align and collaborate with practitioners, there is a lack of economic or political support to make the changes that need to happen; or
  4. Conservation biologists do not commit to engaging themselves in the implementation of their recommendations due to a lack of reward structure for this behaviour and the conflicting roles of academia and conservation.

Arlettaz and colleagues illustrate how to overcome these roadblocks using a case study of their own work on the endangered hoopoe (Upupa epops) in Switzerland, showing how they followed through the recommendations of their work to implementation and had a direct impact on species recovery. They highlight means by which other conservation biologists can do the same.

Read the rest of this entry »


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Categories : conservation, conservation biology, environmental policy, environmental science, management, science, science communication

What the hell is a banteng?

21 02 2011

A few years ago (ok, 6 years), ABC‘s Catalyst did a piece on our banteng research programme in Garig Gunak Barlu National Park in the Northern Territory. The show basically talks about the conservation and management conundrum of having a successful feral species in Australia that is also highly endangered in its native range (South East Asia). Do we shoot them all, or legislate them as an endangered species? It’s for Australians to decide.

I finally got around to uploading it on Youtube. I hope I haven’t contravened some copyright law, but I figure after such a lag, no one will care. I await the imminent contradiction from the ABC’s lawyers…

I hope you enjoy.

For the scientific papers arising from the work, see: Read the rest of this entry »


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Categories : Australia, bushmeat, conservation, extinction, harvest, invasive species, management, population dynamics, research, science, tropical

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