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 fragmentation^1-3.

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.

Figure 1: Road use by cane toads in the Northern Territory, Australia (2). Top panel: frequency of radio-tracked individuals recorded at different distances to the nearest dirt road (25 to 975 m in 50 m intervals). Bottom panel: frequency of toads with body axis aligned at different angles with the main axis of the Arnhem Highway (0º for toads facing the main axis of the road, to |90|º for toads facing perpendicular to the right or left of the road). Most toads were found within 25 m of dirt roads, and facing -10º to 10º to the highway axis.

Brown and colleagues⁴ illustrate the latter scenario with cane toads (formerly Bufo marinus; now Rhinella marina) in Australia. This species was introduced to Queensland in the 1930s to control (unsuccessfully) insect pests in sugar cane fields⁵. Nowadays, Aussie cane toads outnumber the human population in China, occupy a surface equivalent to 100 million soccer stadia, and only in 2009 crossed the border of Western Australia, > 2,500 km from the release point⁶ [see Rick Shine’s cane toad lab research]. For over 300 nights, Brown et al. radio-tracked 49 adult toads in farmland and eucalyptus forest in the Northern Territory. They found that these animals adjusted their movements to the local network of roads. In half of the records, toads were seen on or near dirt roads, mainly following those portions of the roads in the Northwest direction of progression of the invading front (Figure 1).

With an independent sample, they observed that the body axis of most individuals found near a highway was aligned with the principal axis of the road (Figure 1), giving evidence that the animals were moving relative to the trajectory of the highway. Undoubtedly, roads confer demographic benefits that compensate the > 200 tonnes of toads killed on the roads in (only) Queensland every year.

The invader’s backpack

Among the panoply of exotic species that are detrimental globally outside their native ranges⁷, the fungus Phytophthora lateralis is another self-explanatory example of road-loving biological invasion⁸. Rivers disperse the spores of this fungus. The spores then parasitise the roots of tree species along riverbanks and beyond (i.e., during floods), resulting in fulminating rot of the entire root system. In Oregon and California, spores have spread in most rivers in the mud stuck to vehicles and people’s shoes walking along local dirt roads. The disease was first recorded in the 1920s in Seattle in a plantation of Port Orford cedars (Chamaecyparis lawsoniana). It has since caused massive mortality of juvenile to centenary cedars in the conifer forests of Western USA, and has ruined a multi-million-dollar export of wood and ornamental trees (by means of which the fungus has already reached, at least, Asia and Europe).

Roads also contribute to the spread of insect and plant pests and human diseases^1,3. In the case of cane toads, dirt roads in the Northern Territory might be assisting in the dispersal of their toxicity (arguably the toad’s worst ecological impact⁶), present in all developmental stages (egg, tadpole, toadlet, and adult), especially for adults because toxicity increases with size. Up to 27 species of vertebrates have been reported to die from ingestion of cane toads⁵ – thus, at a population level, it is predictable that the worst ravages will occur in apex predators able to catch larger (and more toxic) toads, such as elapid snakes, varanid lizards, the freshwater crocodile (Crocodylus johnstoni) and quolls (Dasyurus spp.)⁶.

Surely we all want roads that are safe and (as much as possible) benign for biodiversity. Taylor and Goldingay² have recently reviewed the state of the art of published research into roads and wildlife worldwide, with the following highlights:

• studies on large ungulates and carnivores predominate, partly due to rocketing insurance and medical costs after collisions;
• road-crossing structures for wild animals are being widely applied, although population benefits remain poorly understood;
• behavioural avoidance with genetic and metapopulation implications occurs in some species, calling for landscape road planning;
• focused management actions are needed for globally threatened species like amphibians (surely not cane toads),
• poor experimental designs across the board.

It caught my eye that the three reviews I cite^1-3 did not encompass road impacts on subterranean ecosystems⁹ – a dark oasis of living wonders¹⁰ and reservoir of > 30 % (98 % along with glaciers) of available freshwater globally¹¹. Clearly, to those who build roads (from the politician to the engineer), environmental impact assessment should take into account their multiple ecological impacts, and not only along the route itself^2,3.

Next time you hit the road, be aware; you are never alone.

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1. S. C. Trombulak and C. A. Frissell, Conserv Biol 14 (1), 18 (2000) doi:10.1046/j.1523-1739.2000.99084.x
2. B. D. Taylor and R. L. Goldingay, Wildl Res 37 (4), 320 (2010) doi:10.1071/WR09171
3. W. F. Laurance, M. Goosem, and S. G. W. Laurance, Trends Ecol Evol 24 (12), 659 (2009) doi:10.1016/j.tree.2009.06.009
4. G. P. Brown, B. L. Phillips, J. K. Webb et al., Biol Conserv 133 (1), 88 (2006) doi:10.1016/j.biocon.2006.05.020
5. C. Lever, The Cane Toad. The History and Ecology of a Successful Colonist. (Westbury Academic and Scientific Publishing, Otley, UK, 2001)
6. R. Shine, Quart Rev Biol 85 (3), 253 (2010) doi:10.1086/655116
7. S. Lowe, M. Browne, and S. Boudjelas, Aliens 12, S1 (2000)
8. E. M. Hansen, Boreal Environ Res 13, 33 (2008); E. M. Hansen, D. J. Goheen, E. S. Jules et al., Plant Disease 84 (1), 4 (2000) doi:10.1094/PDIS.2000.84.1.4; E. S. Jules, M. J. Kauffman, W. D. Ritts et al., Ecology 83 (11), 3167 (2002)
9. M. Knez and T. Slabe, in Encyclopedia of Caves and Karst Science, edited by J. Gunn (Palgrave Macmillan, London, UK, 2004), pp. 419
10. J. Gibert and L. Deharveng, BioScience 52 (6), 473 (2002) doi:10.1641/0006-3568(2002)052[0473:SEATFB]2.0.CO;2; D. C. Culver and B. Sket, J Cave Karst Stud 62 (1), 11 (2000)
11. D. L. Danielopol, C. Griebler, A. Gunatilaka et al., Environmental Conservation 30 (2), 104 (2003) doi:10.1017/S0376892903000109
12. B. L. Phillips, G. P. Brown, J. K. Webb et al., Nature 439 (7078), 803 (2006) doi:10.1038/439803a
13. N. Sallam, Aust J Entomol 50 (3), 300 (2011) doi:10.1111/j.1440-6055.2010.00807.x

www.sumatranforest.org

Bill Laurance asked me to reproduce his latest piece originally published at Yale University‘s Environment 360 website.

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We live in an era of unprecedented road and highway expansion — an era in which many of the world’s last tropical wildernesses, from the Amazon to Borneo to the Congo Basin, have been penetrated by roads. This surge in road building is being driven not only by national plans for infrastructure expansion, but by industrial timber, oil, gas, and mineral projects in the tropics.

Few areas are unaffected. Brazil is currently building 7,500 km of new paved highways that crisscross the Amazon basin. Three major new highways are cutting across the towering Andes mountains, providing a direct link for timber and agricultural exports from the Amazon to resource-hungry Pacific Rim nations, such as China. And in the Congo basin, a recent satellite study found a burgeoning network of more than 50,000 km of new logging roads. These are but a small sample of the vast number of new tropical roads, which inevitably open up previously intact tropical forests to a host of extractive and economic activities.

“Roads,” said the eminent ecologist Thomas Lovejoy, “are the seeds of tropical forest destruction.”

Despite their environmental costs, the economic incentives to drive roads into tropical wilderness are strong. Governments view roads as a cost-effective means to promote economic development and access natural No other region can match the tropics for the sheer scale and pace of road expansion. resources. Local communities in remote areas often demand new roads to improve access to markets and medical services. And geopolitically, new roads can be used to help secure resource-rich frontier regions. India, for instance, is currently constructing and upgrading roads to tighten its hold on Arunachal Pradesh state, over which it and China formerly fought a war.

Of course, roads are not just an environmental worry in the tropics. In forested areas of western North America, one of the best predictors of wildfire frequency is the density of roads. In Siberia, road expansion is promoting a sharp increase in logging and forest fires. And new roads in the Arctic could potentially alter epic mammal migrations.

But no other region can match the tropics for the sheer scale and pace of road expansion and the degree of environmental change roads bring. Road building has a range of direct impacts on rainforest ecology. In wet tropical environments, the cut-and-fill operations associated with road construction can impede streams, increase forest flooding, and drastically increase soil erosion. Roads also discharge chemical and nutrient pollutants into local waterways and provide avenues of invasion for many disturbance-loving exotic species.

Roads that cut through rainforests can also create barriers for sensitive wildlife, many of which are ecological specialists. Studies have shown that even narrow (30 m-wide), unpaved roads drastically reduce or halt local movements for scores of forest bird species. Many of these species prefer deep, dark forest interiors; they have large, light-sensitive eyes and avoid the vicinity of road verges, where conditions are much brighter, hotter, and drier. A variety of other tropical species — including certain insects, amphibians, reptiles, bats, and small and large mammals — have been shown to be similarly leery of roads and other clearings.

And by bringing naïve rainforest wildlife into close proximity with fast-moving vehicles, roads can also promote heavy animal mortality. For some creatures, especially those with low reproductive rates, roads could potentially become death zones that help propel the species toward local extinction.

Although the direct effects of roads are serious, they pale in comparison to the indirect impacts. In tropical frontier regions, new roads often open up a Pandora’s box of unplanned environmental maladies, including illegal land colonization, fires, hunting, gold mining, and forest clearing.

“The best thing you could do for the Amazon,” said the respected Brazilian scientist Eneas Salati, “is to bomb all the roads.”

In Brazilian Amazonia, my colleagues and I have done studies showing that around 95 % of all deforestation occurs within 50 km of highways or roads. Human-lit fires increase dramatically near Amazonian roads, even within many protected areas. In Suriname, most illegal gold mining occurs near roads, whereas in tropical Africa we have found hunting to be so intense near roads that it strongly affects the abundance and behaviour of forest elephants, buffalo, duikers, primates, and other exploited species. Roads can sharply increase trade in bushmeat and wildlife products; one study found that eight killed mammals were transported per hour along a single road in Sulawesi, Indonesia.

Paved highways are especially dangerous to forests. They provide year-round access to forest resources and reduce transportation costs, causing larger-scale impacts on forests and wildlife than do unpaved roads, which tend to become impassable in the wet season. The proposed routes of new highways often attract swarms of land speculators who rush in to buy up cheap forest land, which they then sell to the highest bidder.

Perhaps the most damaging aspect of paved highways is that they spawn networks of secondary roads, which spread further environmental destruction. For instance, the 2,000 km-long Belem-Brasília highway, completed in the early 1970s, has today evolved into a spider web of secondary roads and a 400 km-wide swath of forest destruction across the eastern Brazilian Amazon. As my colleagues and I showed in a 2001 study published in Science, large expanses of the Amazonian forest could be fragmented by the advance of new highways and roads in Brazil. According to our models, by the year 2020, rates of forest destruction would rise by up to 500,000 ha per year, and the area of forest that remained in large, unfragmented tracts — exceeding 100,000 km² — would decline by 36 %.

Can the environmental impacts of tropical roads be minimized? In theory, the answer is “Yes, partially.” Frequent culverts can reduce the effects on streams and hydrology. Impacts on animal movements can be reduced by keeping road clearings narrow enough so that canopy cover is maintained overhead, providing a way for arboreal species to cross. In high-priority areas, such as certain national parks, rope-bridges are being used to facilitate road crossings of monkeys and possums. For small ground-dwelling species, culverts beneath roads can allow road-crossing movements, and even large animals such as Asian elephants will use highway underpasses that are designed to be wildlife-friendly.

Measures also exist to limit the devastating indirect impacts of roads, such as illegal land colonization and forest clearing. One of the most vital steps is to establish legally parks or reserves along road routes in advance of road construction. Such reserves often substantially reduce forest incursions, though they rarely halt them entirely. Another promising idea is to promote rail roads rather than highways in tropical wilderness regions. Because railroads stop only at fixed locations, the spatial patterns of forest exploitation and movement of forest products can be more easily controlled and monitored than with roads.

In practice, however, limiting the environmental impacts of roads in developing nations is expensive and risky. Tropical nations rarely have the institutional capacity, human capital, or financial resources to adequately manage development in their remote frontier regions, frequently leading to a “resource grab” revolving around illegal trade and outright theft of natural resources, which is greatly facilitated by road expansion.

When it comes to tropical roads, I believe three conclusions are inescapable. First, highways and roads are the single biggest factor determining the pattern and pace of tropical forest destruction. New roads that slice deep into intact forest tracts are especially devastating.

Second, among the many human drivers of environmental change, road building is one of the most readily amenable to policy modification. In practical terms, it is far easier to cancel or relocate a road project than it is to, say, reduce human overpopulation or halt harmful climate change.

Finally, if we hope to maintain intact tropical forests and their vital ecosystem services and biodiversity, then we simply must get serious about tropical roads. And there is only one real solution: carefully plan and limit frontier road expansion.

How can this be achieved? First, we need to sensitize political decision-makers, economists, infrastructure planners, and the general public about If we hope to maintain intact tropical forests, then we must get serious about tropical roads. the myriad environmental costs of road expansion, especially into intact forests. The biggest road projects are often being supported by international lenders — such as the Asian, African, and Inter-American development banks — and by foreign aid doled out by China, the U.S., and the European Union. Educating such decision-makers needs to be done both generally and on a project-by-project basis.

When I was president of the Association for Tropical Biology and Conservation, one of my key goals was to use the organization’s scientific expertise and credibility to combat some of the most environmentally risky plans for frontier road expansion. We were especially active in critiquing plans to punch new roads into the cores of national parks, such as Yasuní in Ecuador, Kerinci Seblat in Indonesia, and the Serengeti in Tanzania.

Another key priority should be better frontier law enforcement and forest monitoring, given that much road building in tropical nations is illegal or unplanned. Special attention should be focused on the more-aggressive timber, oil, gas, and mineral corporations, many of which are known to engage in bribery and collusion in their efforts to gain unbridled access to forest resources.

There is also a dire need to improve environmental impact assessments (EIAs) for planned roads. In Brazil, for instance, EIAs for several major Amazonian highways focused only on a narrow strip along the road route itself, while completely ignoring the devastating indirect effects of roads. Similarly, EIAs for major development projects, such as large mines and hydroelectric dams, often ignore the impacts of road proliferation that such projects inevitably promote.

Finally, given that tropical deforestation is a massive source of greenhouse gas emissions, international carbon-trading funds should be used to better plan and mitigate road projects, to establish new protected areas in advance of road construction, and to halt the most ill-advised road projects altogether. In the end, the easiest and most cost-effective way to limit the manifold pressures from roads may be simply not to open Pandora’s box in the first place.

William F. Laurance

Before I get into specifics, I have to say that one thing we conservation biologists tend to bang on about is that MORE SPECIES = BETTER, regardless of the ecosystem in question. We tend to value species richness as the gold standard of ecosystem ‘health’ and ‘resilience’, whether or not there is strong empirical evidence in support. It’s as if the more-is-better mantra strikes an intuitive chord and must, by all that’s ecologically right in the world, be true.

Of course, measuring what is ‘better’ is a difficult task, especially when we are talking about complex ecosystems comprising thousands, if not millions, of species. Does ‘better’ refer to the most temporally stable, the most genetically diverse, the most resilient to perturbation, or the provider of the greatest number of functions and hence, ecosystem services?

It’s up to you, but all these things tend to be difficult to measure for a large number of species and over time scales of sufficient duration to measure change. So the default for plants (i.e., the structural framework of almost all ecosystems) I guess has come down to a simpler measure of success – ‘productivity’. This essentially means how much biomass is produced per unit area/volume per time step. It’s not a great metric, but it’s probably one of the more readily quantifiable indices.

Enter the so-called ‘diversity-productivity relationship’, or ‘DPR’, which predicts that higher plant species diversity should engender higher net productivity (otherwise known as the ‘net biodiversity effect’).

Nice idea, and one that is especially attractive in this day of carbon accounting (forest carbon sequestration as offsets to industrial and transport greenhouse gas production). If true, the net biodiversity effect is adequate justification for maximising species diversity in carbon plantings such that both carbon sequestration and biodiversity value are maximised – the best bang for your planting buck.

The problem is that it’s not even close to being a theory in ecology, let alone a law. In fact, the hypothesis has very mixed empirical support, and the majority of it is in manipulated and simplified grasslands, with no net effect, or even negative relationships, reported for natural forest stands. Not a good sell really if you’re trying to convince a policy maker that more species are better to maximise productivity, and hence, carbon uptake.

Enter Yu Zhang and colleagues and their recently published (online) paper: Forest productivity increases with evenness, species richness and trait variation: a global meta-analysis. Now, I’m a big fan of meta-analyses to answer big questions; there’s nothing like a lot of disparate studies collated to provide insight into broad-scale pattern (e.g., see our recent meta-analysis on the value of primary forests for tropical biodiversity published in Nature last year).

And that’s exactly what they did – Zhang and colleagues collated diversity-productivity data from 54 forest studies to determine the overall ‘average’ direction of the diversity-productivity relationship. Using boosted-regression trees (and slick way to deal with complex multi-variate data), their overall conclusion was that ‘polycultures’ (i.e., many species) were more productive than ‘monocultures’ (single-species stands). So much for the DPR debate in forest ecosystems.

More interestingly perhaps was that the biodiversity metric used dictated the strength of effect found. Even though there was a positive richness relationship (more species = higher productivity), it plateaued after a certain threshold number of species. However, when using ‘evenness’ as the measure of ‘diversity’ (i.e., a metric which includes relative abundance of each species in system), stands that were more even (i.e., not dominated by a few common species) were more productive, and this metric explained a much higher component of the variance in productivity than richness alone. This means that a simple list of species doesn’t really indicate the full potential of the stand because of things like functional redundancy. Finally, they found no evidence for a deviation of the relationship among biomes, suggesting that the effect is global and real.

Now there are a lot of fine details in the analysis that complicate matters, but I think the take-home message is clear. This is a hugely important finding and one that all conservation ecologists should be able to cite when justifying the essential role of diversity in ecosystem function.

CJA Bradshaw

I suppose the delve from historical/modern ecology into prehistory was inevitable given (a) my long-term association with brain-the-size-of-a-planet Barry Brook (who, incidentally, has reinvented his research career many times) and (b) there is no logic to contend that palaeo extinction patterns differ in any meaningful way from modern biodiversity extinctions (except, of course, that the latter are caused mainly by human endeavour).

So while the last, fleeting days of my holiday break accelerate worringly toward office-incarceration next week, I take this moment to present a brand-new paper of ours that has just come out online in (wait for it) Quaternary Science Reviews entitled Robust estimates of extinction time in the geological record.

Let me explain my reasons for this strange departure.

It all started after a few drinks (doesn’t it always) with Alan Cooper, Chris Turney and Barry Brook when we were discussing the uncertainties associated with the timing of megafauna extinctions – you might be aware that traditionally there have been two schools of thought on late-Pleistocene extinction pulses: (1) those who think there were mainly caused by massive climate shifts not to dissimilar to what we are experiencing now and (2) those who believe that the arrival of humans into naïve regions lead to a ‘blitzkrieg‘ of hunting and overkill. Rarely do adherents of each stance agree (and sometimes, the ‘debate’ can get ugly given the political incorrectness of inferring that prehistoric peoples were as destructive as we are today – cf. the concept of the ‘noble savage‘).

As most readers of CB might appreciate, I generally do not subscribe to the ‘one equation fits all’ hypothesis when it comes to extinctions. Close inspection of the historical record general supports the conclusion that most extinctions arise from a perverse synergy of drivers which increase kill rates beyond the mere sum of their individual effects. Thus, why human overkill and a series of large climate shifts could not have ‘worked’ in unison to drive the major extinction events recorded in the fossil record over the last 100,000 years or so has no real theoretical justification; it seems that many engaged in the debate adhere exclusively to one view or the other. To us, this is clearly a gross over-simplification.

But as I am want to do, I digress (there will be much more of this in the next few months as Alan, Chris, Barry and I finalise a few analyses on this subject for the Holarctic, late-Pleistocene megafauna extinctions). The issue about which I am writing today (and the subject of the paper in question) is the precursor to all this debate, for how can you possibly determine the contribution of possible drivers if you don’t really know when species x went extinct?

You can see where I’m going with this if you know a little about fossils. As you can appreciate, most dead things don’t fossilise, and even if they do, the rate and extent at which fossilisation occurs can be extremely variable. Plus, there’s the added complication of finding the bloody things (we haven’t yet dug up the entire surface of the planet). So the probability of an animal dying in the right place, having the right conditions for fossilisation, persisting through time in some state of preservation and being found by one of those strange people who like digging for the fossilised remains of long-dead creatures (that bizarre breed of human known as a ‘palaeontologist’) is mind-numbingly small.

Thus, trying to figure out the ‘last’ time extinct species x walked the planet isn’t as straight-forward as it might initially seem simply by dating the most recent fossil in a series of fossils. Who’s to say the ‘most recent’ is indeed that? Then, off course, there’s the added uncertainty in the dating method itself; radiocarbon methods used to date fossils from several thousand to about 60,000+ years ago have a certain margin of error that increases the farther back in time you go.

You might be beginning to get the picture – fossil records generally are pretty crap for inferring extinction times.

Now, several clever people have attempted to incorporate all this uncertainty together in fairly sophisticated statistical models to estimate the time that a species actually went extinct. One of the most famous was the application by Solow and Roberts of the Weibull distribution to a series of known dodo sightings prior to their demise (although in this case, Solow and Roberts assumed that there was no uncertainty in the dates); Solow and colleagues went on to modify the approach to incorporate radiocarbon dating uncertainty. And there are others.

However, all approaches developed to date make certain assumptions about the underlying distribution of the probability of fossilisation and discovery, and few make any attempt to correct for sampling artefacts in the time series themselves (i.e., how many fossil records are there?). Enter us.

Our paper describes a new method built on one constructed by McInerney and colleagues that incorporates most of the uncertainty, as well as making no assumptions about the underlying distribution. We call it the ‘GRIWM’ method (‘Gaussian-resampled inverse-weighted McInerney’ – I know, a clumsy mouthful, but the acronym helps) because it resamples the dates within their radiocarbon confidence bounds, and it weights the most recent fossils more heavily than older ones to account for sample-size differences among series. The McInerney method itself is based on the sighting interval (time between fossil discoveries) to predict the probability of another one being found.

While the maths might be a little impenetrable for some, it’s really a rather straight-forward approach that I hope will get a lot of use. The links to the modern biodiversity crisis are manifold – if we can decipher the set of conditions leading to some of the biggest extinction events in the history of the Earth, we should be better placed to prevent some of the worst ravages in the future

CJA Bradshaw

Paul has recently blogged about the ‘species’ concept as it relates to DNA barcoding, which I highly recommend. It also prompted me to write this post because now the video of the discussion is available online (see below).

Now, the panel was a bit of a funny set-up in a way – I was really one of the only ‘conservation biologists’ represented (Patrick O’Connor and Andy Lowe perhaps excepted), with the rest mainly made up of molecular people (Pete Hollingsworth, Bob Hanner, Karen James) – and I was told prior to the ‘debate’ that I was meant to be the contrarian (i.e., that there is no role for DNA barcoding in conservation).

Fundamentally, I don’t actually embrace the contrarian view on this one given that I see no reason why DNA barcoding can’t enhance or refine our conservation knowledge and skills. But the ‘debate’ did raise some important issues about technological advancements in the application of conservation science to real conservation.

I suppose that prior to getting stuck into the polemic I should define DNA barcoding for the uninitiated; it’s a basic technique that analyses short sequences of DNA with the sole purposes of identifying from which species they come. Imagine walking through the bush with a barcode scanner and pointing at random species you see and getting an instant identification read-out without actually knowing the species beforehand. You can see why it’s called ‘barcoding’ because it is like running products through the check-out to get instant price details.

Some of the advantages for conservation should be immediately obvious – ‘forensics’ of the wildlife or illegal timber trade can be enhanced by letting authorities know the origin and pathway of illegally imported or marketed animal or plant products. This can give bodies like customs and quarantine departments a big legal stick to smash poaching rings, et cetera. Another is determining the presence of a rare species that is difficult or impossible to survey – for example, identifying DNA fragments of rare fish in samples of river water. Once identified using DNA barcoding, a legal argument to preserve that habitat on the basis of threatened wildlife legislation can be made without the expense and uncertainty of traditional wildlife surveys.

I suppose the main point of contention about DNA barcoding is that it merely refines our capacity to survey species we probably already know are in trouble. I submitted during the discussion that we could probably kill every single conservation biologist in the world and not really handicap ‘conservation implementation’ in any major way because we have the main aspects of the science sorted (fragmentation is bad; more habitat area = more species; climate change is bad; invasive species are bad; too few individuals is bad; small populations tend to go extinct; drivers of extinction synergise to make things worse – see full list on Conservation Classics). The principal conservation science discoveries have been made; now we need to manage the resource consumption of 7 billion humans more than anything else. You can also read more about conservation science ‘mucking around the edges‘ in a previous post here on CB.

Another potentially questionable application of barcoding to conservation is that it merely tells us if something is there, not how many or in what state. With a simple binary output, we lack some essential information regarding the value of an area based on mere presence/absence. Certainly we do now do area prioritisation based largely on presence/absence data, but how many more cryptic species identifications do we need to prioritise habitats for preservation?

Those somewhat philosophical beefs aside, I’m still very much in support of the concept of quantifying species better than the somewhat subjective and categorical binomial genus-species system we currently use. I’m also excited by the prospect of using DNA barcoding to quantify ecosystem health better by measuring soil and water microbia composition, and perhaps even starting to get a handle on soil fungus diversity. If we can even improve DNA barcoding to become ‘q-barcoding’ that quantifies relative abundance in addition to identification, we’ll really have a massively important tool for measuring ecosystem and species health.

I’ll be interested in CB readers’ opinions on the subject.

CJA Bradshaw

Filed under: anthropocene, conservation, DNA, ecosystem function, genetics, mycorrhiza ]]> http://conservationbytes.com/2012/01/05/does-conservation-biology-need-dna-barcoding/feed/ 1 -34.917731 138.603034 -34.917731 138.603034 CJAB dna http://conservationbytes.com/2011/12/30/cartoon-guide-to-biodiversity-loss-xiv/ http://conservationbytes.com/2011/12/30/cartoon-guide-to-biodiversity-loss-xiv/#comments Fri, 30 Dec 2011 02:16:00 +0000 CJAB http://conservationbytes.com/?p=6570 ]]> The last post of 2011, I thought I’d focus on the lighter side (that is to say, my brain is muddled by the lovely break from academia, so I don’t really feel like investing too much cerebral energy). Here, therefore, are the latest six cartoons… (see full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here). May fewer species go extinct in 2012 than 2011…

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© 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!

His latest regurgitation of spectacularly uninformed and politically motivated, anti-environmental vomit couldn’t have missed the point more on the Macquarie Island feral eradication programme. Most would agree that despite our general failing of biodiversity conservation, conservation biologists have had a fair share of major wins with island pest eradications; indeed, at times it seems the only thing we can get right is killing the baddies we were originally responsible for introducing.

Now, I’m no fan of the Tasmanian legislators and government drones who for years delayed or severely under-appreciated science to inform sound environmental policy when it came to Macquarie Island (indeed, I would go so far as to say that the established environmental autocracy in the Tasmanian government is one of the principal enemies of conservation because of their entrenched anti-science stance), but for once, they finally got around to doing something good with this ~ million-dollar programme.

And I have some history there too – I was stationed on Macquarie Island over 4 years from 1999-2004 during my postdoctoral fellowship, during which time I worked on many aspects of elephant seal population and behavioural ecology (see associated publications here). In my last year there, I was shocked upon my return to the island after an 18-month stint back in mainland Australia about just how much damage the rabbits had done after the last cat had been shot a few years before. I was so moved that I wrote a popular article on the matter to bring it to the public’s attention – you can read that article (published in Australasian Science) here for more background information.

For the ultra-right wing Senator Abetz to turn this success into his own political poisoned arrow is, to be perfectly honest, an environmental crime in its own right. Using the weak argument that some protected species have suffered as a consequence is the classic tool of the so-called ‘environmentalists’ who would rather focus on a single species (or even individual) while the rest of biodiversity melts into extinction (see related post here). We just don’t have time for this nonsense, and this is why we have to consider uncomfortable choices such as triage and controversial energy-generation technology.

I’m not for a moment insinuating that Senator Abetz truly feels for the poor seabirds who had the misfortune of swallowing a bit of poisoned bait in the quest to return their island to its former pristine biodiversity greatness; rather, I think he used the weak and uninformed argument for his own political gains (a double travesty). We have to move past this double-dipped bullshit if we want to make some real gains for biodiversity in Australia.

CJA Bradshaw

© WWF

Apologies for the slow-down in postings this past week – as many of you know, I was attending the International Congress for Conservation Biology in Auckland. I’ll blog about the conference later (and the stoush that didn’t really occur), but suffice it to say it was very much worthwhile.

This post doesn’t have a lot to do per se with the conference, but it was stimulated by a talk I attended by Conservation Scholar Stuart Pimm. Now, Stuart is known mainly as a tropical conservation biologist, but as it turns out, he also is a champion of temperate forests – he even sits on the science panel of the International Boreal Conservation Campaign.

I too have dabbled in boreal issues over my career, and most recently with a review published in Trends in Ecology and Evolution on the knife-edge plight of boreal biodiversity and carbon stores. That paper was in fact the result of a brain-storming session Navjot Sodhi and I had one day during my visit to Singapore sometime in 2007. We thought, “It doesn’t really seem that people are focussing their conservation attention on the boreal forest; how bad is it really?”.

Well, it turns out that the boreal forest is still a vast expanse and that there aren’t too many species in imminent danger of extinction; however, that’s where the good news ends. The forest itself is becoming more and more fragmented from industrial development (namely, forestry, mining, petroleum surveying and road-building) and the fire regime has changed irrevocably from a combination of climate change and intensified human presence. You can read all these salient features here.

So, back to my original thread – Stuart gave a great talk on the patterns of deforestation worldwide, with particular emphasis on how satellite imagery hides much of the fine-scale damage that we humans do to the world’s great forests. It was when he said (paraphrased) that “50,000 km² of boreal forest is lost each year, but even that statistic hides a major checkerboard effect” that my interest was peaked.

So I finally come to the point of this post. In the special issue of essays devoted to the memory of Navjot Sodhi to be published in Biological Conservation in early 2012 (see also the previous post on another paper of ours that will appear in that issue), Ian Warkentin and I (Ian co-authored the first paper in TREE mentioned above) have written a ‘boreal’ tribute to Navjot that has just come out online early.

The paper is entitled A tropical perspective on conserving the boreal ‘lung of the planet’ and in it we describe the little-known fact that despite being one of the world’s top tropical ecologists, like Stuart Pimm, Navjot had his roots in the boreal realm and was keen to apply his expertise to saving its species. So much did he believe this was necessary that prior to his untimely death, Navjot had accepted a posting at the University of Toronto where he was to set a portion of his research focus on developing a hard-hitting boreal conservation programme. Unfortunately, he never made it.

In the essay we describe Navjot’s boreal past and future intentions, and we also highlight another research project currently under way that has impressed me in its scope and breadth. The project is called Ecosystem Management Emulating Natural Disturbance (EMEND) and I believe it is EXACTLY the sort of long-term experiment that needs to be done across the boreal biome to examine how fire, timber harvesting and other human activities interact to change biodiversity and ecosystem resilience. Bit of a coincidental story there – the only reason I knew about EMEND at all prior to writing the essay was that I had the good fortune of meeting John Spence in Guangzhou, China earlier this year for the International Symposium for Biodiversity and Theoretical Ecology organised by Fangliang He. John gave a wonderful talk describing EMEND, so I just had to include a blurb about it in our essay.

And good things come to those who dabble. Very soon after the Guangzhou symposium, I was contacted by Jon Moen and Lucy Rist of Umeå University in Sweden about joining their special symposium entitled ‘Boreal Forests in a Sustainable World’ to be held during the EcoSummit 2012 conference in Columbus, USA in September 2012. I’m not entirely sure what analysis I’ll be presenting with Ian, but it probably will be along the lines of measuring the fragmentation component more precisely (perhaps in collaboration with Stuart Pimm if he’s keen). Jon and Lucy have also organised a pre-EcoSummit meeting in Sweden in April that I hope to attend. Should be interesting.

Enough waffle for a Monday morning. If you’d like a PDF copy of the boreal ‘lung’ essay, just e-mail me.

CJA Bradshaw

http://goo.gl/KZ50o

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

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

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

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

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

• We were somehow promulgating that conservation decisions should be made solely on the back of SAFE (we never said this, nor support such a crazy idea); we merely point out that SAFE provides information that the Red List categories do not.

• The IUCN threshold abundance criteria (mostly inherent in Criteria C & D) are not arbitrary and in fact based in a sound, empirically derived manner:

Well, we had a look at this in the original paper by Georgina Mace and colleagues justifying the abundance thresholds. First, While some values seem to have some logical basis and are in fact EXACTLY in line with our previous work on minimum viable population size supporting the ‘thousands’ (median: 5000) mark (in other words, our detractors have, retro-actively, agreed with us), all other thresholds are based on a theoretical paper published by Russ Lande in 1993 entitled: Risks of population extinction from demographic and environmental stochasticity and random catastrophes (American Naturalist 142: 911–927). Now, Russ is a bit of a theoretical ecology god, and the paper is great; however, the practicality (and biological reality) of the thresholds he derives can be questioned. His theoretical estimates are based on an unstructured, exponential model with a ceiling carrying capacity; while certainly informative, relying on such a relatively simple model that really only describes the effects of demographic stochasticity (kicking in at very small population sizes) should have rung some alarm bells. On the contrary, our analyses examining fully standardised MVP estimates from a wide range of taxa and based on empirical measurements give a more conservatively based estimate of a generalisable extinction-risk threshold. Thus, we come back to our original point – pegging a species’ population size to a generalised target makes intuitive sense and goes well beyond the theoretical (and simplistic) abundance threshold criteria provided in the Red List (but see previous point about not relying solely on SAFE – ours is an added dimension, not a replacement).

• Almost NO species are assessed in the Red List based on Category E alone (population viability analysis); SAFE does this implicitly.
• If our detractors are in fact so against any threshold criteria, then we propose that the power brokers of IUCN Red List should do the right thing and dump categories D and E entirely (as well as components of C). We would advise against this, but the corner in which they appear to be painting themselves argues for this outcome.

Now, I do not want to give readers the impression that my invective is in any way a criticism of our detractors’ research. I am a HUGE fan of many of them (e.g., the legend of Mace, the brilliance of McCarthy, the numerical genius of Akçakaya), I have published with some of them, and I clearly think that much of their research is directly and indirectly responsible for reducing extinctions. However, I am increasingly surprised by the blockade they keep putting up against the elegant simplicity of SAFE and its potential applications.

So, back to the conference in Auckland next week. I will expand on some of these issues and present some more data supporting our case. I imagine a few stone throwers will be in the crowd, so question time should be entertaining ;-).

CJA Bradshaw

http://goo.gl/ogdT8

I suspect a lot of ConservationBytes.com readers will be attending the imminent 25^th International Congress for Conservation Biology to be held in Auckland from 5-9 December 2011 (it was to be held in Christchurch, but the venue was changed after that city fell down). I’ve now been to 3 previous ICCBs myself, and it should prove to be a good, informative (and fun) meeting.

I’ll be giving a talk or two, as will some of my students and postdocs, but I’m not spruiking those here (but you’re all invited, of course).

The main reason for this short post today is to advertise for Version 2 of our (i.e., Bill Laurance and me) popular ‘Supercharge Your Science‘ workshop. Yes, the organising committee of the ICCB decided it was a good idea to accept our application to repeat our previously successful series of presentations extolling the virtues of positive and controlled media interactions, social media and good writing techniques for ‘supercharging’ the impact of one’s science. You can read more about the content of this workshop here and here.

The description of the workshop (to be held from 19.00 – 21.00 on 6 December in the SkyCity venue) on the ICCB website is:

In this dynamic and fun two-hour workshop, we will highlight a range of strategies for increasing your scientific impact and productivity. This workshop emphasises transcending scientific audiences to engage the popular media and general public, and thus is highly relevant to the theme of SCB 2011. The workshop is divided into three parts. Part 1 is a 25-minute talk by Prof. William Laurance entitled “Reaching Out: Maximizing Your Public Impact“. In it Laurance highlights a variety of approaches for engaging journalists, getting broader recognition for your work, and becoming a science and conservation leader. Part 2, by Prof. Corey Bradshaw, is a timely 30-minute talk entitled “Using Social Media to Supercharge Your Science“. Bradshaw tells how blogging, tweeting, webzines, Facebook, and other social media can dramatically increase your ability to reach a diverse audience. Part 3, by Laurance, is an engaging 35-minute talk entitled “How to be More Prolific: Strategies for Writing and Publishing Scientific Papers“. Laurance, the author of over 300 scientific and popular articles, highlights strategies for writing better and more easily, producing dynamic research, and dealing with editors and reviewers. The symposium includes a 15-minute coffee break and 15 minutes for questions and discussion. Laurance and Bradshaw have run this workshop twice previously to rave reviews.

Apparently the workshop is free (aren’t we generous?), requires no pre-registration, and is open to all. If you want to get this side of your science pumping, but all means, we encourage you to come along.

CJA Bradshaw (also on behalf of Bill Laurance)