Of course we need to save endangered species: a response

I spend a lot of time thinking about the related topics of conservation, biodiversity, and evolution, so I was interested to see an editorial in the Washington Post on precisely those issues. The article, "We don’t need to save endangered species. Extinction is part of evolution" by Alex Pyron, presents a misrepresentative and potentially harmful position about the future of the earth's biota.

Pyron begins by stating that "Evolution loves death." Selection necessarily means the success of one variant at the expense of others, and today's living creatures are the survivors of an ongoing battle for existence. Extinction is not a modern phenomenon by any means. There have been five mass extinctions, including the glaciation of Gondwana and the impact of an asteroid that lead to the loss of the dinosaurs.

But the 6th great extinction (the Anthropocene extinction - the one we are currently living in) shares little in common with these past events. This is the only extinction that a single species (humans) are primarily responsible for, through activities from habitat conversion or degradation, land fragmentation, warming climate, ocean acidification, and human consumption of natural resources. In this context, Pyron's argument seems to be that we ought to retain an anthropocentric viewpoint of conservation as well. That is, we are simply selecting for species that can survive in our wake, and we should feel concern only for those species that we need.

"But the impulse to conserve for conservation’s sake has taken on an unthinking, unsupported, unnecessary urgency. Extinction is the engine of evolution, the mechanism by which natural selection prunes the poorly adapted and allows the hardiest to flourish. Species constantly go extinct, and every species that is alive today will one day follow suit. There is no such thing as an “endangered species,” except for all species. The only reason we should conserve biodiversity is for ourselves, to create a stable future for human beings. Yes, we have altered the environment and, in doing so, hurt other species. This seems artificial because we, unlike other life forms, use sentience and agriculture and industry. But we are a part of the biosphere just like every other creature, and our actions are just as volitional, their consequences just as natural. Conserving a species we have helped to kill off, but on which we are not directly dependent, serves to discharge our own guilt, but little else."

This is hardly an original viewpoint (hastening to the Bible's 'Then God said, “Let Us make man in Our image, according to Our likeness; let them have dominion over the fish of the sea, over the birds of the air, and over the cattle, over all the earth and over every creeping thing that creeps on the earth.'). But it is a short-sighted one. Ignoring more philosophical arguments about the intrinsic value of all species, the arguments presented are problematic and incomplete, and the potential cost could be huge.

Pyron notes that we may be over-estimating the loss of species:

"According to some studies, it’s not even clear that biodiversity is suffering. The authors of another recent National Academy of Sciences paper point out that species richness has shown no net decline among plants over 100 years across 16,000 sites examined around the world."

The study cited by Pyron here does not support the assertion that biodiversity is fine. In fact, Vellend et al (2013) show that at local scales, plant diversity (i.e., the number of plant species; species number being only way of characterizing biodiversity) has been stable. This isn't the same as saying species are not being lost at a global scale. In a follow-up piece (Vellend et al. 2016), the same author notes that at the global scale, "Nonetheless, if we take 142 and 592 as somewhere in the ballpark of extinctions that have occurred between 1600 and 2016, we get extinction rates of 0.98–4.1, 1–2 orders of magnitude higher than the background rate." Outside of plants, Pimm et al. (2014)'s comprehensive review of extinctions in birds, amphibians, and mammals show extinction rates have at least doubled since 1900. These are rates much higher than considered 'natural'. Even when no extinctions have occurred yet, populations are declining rapidly (Ceballos and Ehrlich 2014, Ceballos et al 2017).

An anthropocentric approach also requires complete understanding and control of our environment. Preventing the loss of the species we need or the ecosystems we rely on is not straightforward (as seen by the rarity with which species become 'non-endangered'). Humans are still under-informed about ecosystem services and goods, and what biotic and abiotic interactions are essential to maintain them. The existence of IPBES is a good indicator of how essential and lacking this information is. To confidently state that "Conserving a species we have helped to kill off, but on which we are not directly dependent, serves to discharge our own guilt, but little else" ignores the indirect linkages that might matter, and our lack of knowledge of them.

Further, the philosophy that humans will survive somehow, in the face of losses of biodiversity and changing planetary climate is probably mostly true for the richest members of the planet. Elsewhere, food shortage associated with climate change (eg.) and water shortages (eg.) already threaten individuals in less wealthy countries.

Ironically, Pyron suggests that all we need to make this reality is "moderation".

"The solution is simple: moderation. While we should feel no remorse about altering our environment, there is no need to clear-cut forests for McMansions on 15-acre plots of crabgrass-blanketed land. We should save whatever species and habitats can be easily rescued (once-endangered creatures such as bald eagles and peregrine falcons now flourish), refrain from polluting waterways, limit consumption of fossil fuels and rely more on low-impact renewable-energy sources....We cannot thrive without crops or pollinators, or along coastlines as sea levels rise and as storms and flooding intensify."

But the anthropocentric view of the world that he presents is the opposite of moderation. It favours only humans. In many ways it's the other extreme of the Half-Earth proposal that suggests we set aside half the planet made free of humans. Having been told we don't need to value species beyond our current needs and interests assumes that we will capably and correctly identify those needs and goals, including for time frames beyond our own myopic lifespans. This uncertainty means that a human-centric view may be just as harmful to humans as approaches that ascribe value for biodiversity more value. And humans have proven willing and capable of taking much broader and more effective actions, that accommodate both humans and other organisms. (As FDR said and did: "We have fallen heirs to the most glorious heritage a people ever received, and each one must do his part if we wish to show that the nation is worthy of its good fortune.")

It's frustrating to see this kind of description of biodiversity as though the earth is simply a plus-minus ledger of species – a few lost here, a few gained there.

A conservation baseline is meant to capture an idealized Eden is of course unreasonable. But Pyron's view looks like Hell. ("If this means fewer dazzling species, fewer unspoiled forests, less untamed wilderness, so be it. They will return in time.")

Edit (Nov. 24): the TL:DR is that 
a) I thought the author cherrypicked the ecological literature and downplayed what we know about the loss of biodiversity and the complex/negative effects of human actions; 
b) if the argument is that we should think about biodiversity over timescales of millions of years, humans don't matter anyways; 
c) if we do care about humans, utility values of biodiversity are an acceptable focus of conservation. But it would be misguided to think that we have a perfect understanding of how ecosystems work or a perfect ability to forecast our impacts. For reasons of uncertainty, sampling effects and option value argue that we preserve as much diversity as we can;
d) Non-economic utility values (aesthetic, cultural values) are a good argument for conservation too. Most of us want to leave our children a beautiful planet that is full of life. 

Positive cost-benefit analysis for conservation spending

In a time when most news about human impacts on the Earth's biodiversity seems to be negative, a new paper in Nature provides a glint of good news about our ability to change the current trend of loss. Encouraging new conservation efforts and funding may be contingent on providing evidence that such efforts will actually be effective.

The new report from Waldron et al. (2017) provides evidence for a predictable relationship between conservation spending and reduction of biodiversity loss. They focused on signatory countries of the Earth Summit's Convention on Biological Diversity and Sustainable Development Goals, and developed a pressures-and-conservation-impact’ (PACI) model to predict how biodiversity loss changed in these countries between 1996-2008. Improvements were driven by conservation spending (relativized to reflect differences in buying power between nations) and were counteracted by GDP growth and agricultural expansion. 

Using this model, the authors could predict how the conservation investments made in these nations had affected their loss of biodiversity, as compared to the scenario in which no investment had been made. Amazingly, the median loss of biodiversity per nation was 29% lower than would otherwise have been expected. Over 1996-2008, seven countries even had net biodiversity improvements: Mauritius, Seychelles, Fiji, Samoa, Tonga, Poland and Ukraine.

Fig 1. Map of biodiversity decline scores (BDS) for signatory nations.
"Colours show percentage of all global declines (total BDS) associated with each country. Pie charts show the predicted reduction in decline (in black) if spending had been I$5 million higher (for selected countries); pie size represents the square root of the BDS. Inset shows predicted versus observed BDS (log-transformed) for the continuous model".

They discuss a number of interactions among model terms that capture greater socio-economic complexity - for example, the impacts of GDP growth on biodiversity loss are lower when a country's base GDP is very low. Such large scale studies naturally face data limitations - here, they use mammal and bird Red List status changes to develop a quantitative measure of biodiversity loss. Other taxa presumably show similar trends, but we lack the data to incorporate them at this moment.

Hopefully by demonstrating this cost-benefit analysis for conservation actions, Waldron et al. (2017) encourage future 'investors' as to the payoff of spending on conservation. 

Reductions in global biodiversity loss predicted from conservation spending. Anthony Waldron, Daniel C. Miller, Dave Redding, Arne Mooers, Tyler S. Kuhn,  Nate Nibbelink, J. Timmons Roberts, Joseph A. Tobias & John L. Gittleman. Nature (2017). doi:10.1038/nature24295. 

Progress on biodiversity-ecosystem function requires looking back

Williams, L. J., et al. 2017. Spatial complementarity in tree crowns explains overyielding in species mixtures. - Nature Ecology & Evolution 1: 0063.

It seems at times that the focus on whether biodiversity has a positive relationship with ecosystem functioning has been a bit limiting. Questions about the BEF relationships are important, of course, since they support arguments for protecting biodiversity and suggests a cost of failing to do so. But as a hypothesis ('higher diversity is associated with higher functioning'), they can be rather one-dimensional. It's easy to think of situations in which other types of BEF relationships (neutral, negative) exist. So is it enough to ask if positive BEF relationships exist?

It’s nice then that there is increasingly a focus on identifying mechanisms behind BEF relationships, using both theory and empirical research. A new paper along these lines is “Spatial complementarity in tree crowns explains overyielding in species mixtures” from Laura Williams et al. (2017). "Overyielding" is the phenomenon in which greater total biomass is produced in a mixture of species compared to the expectation based on their biomass production in monoculture. Overyielding would suggest a benefit in maintaining polycultures, rather than having monocultures, and is a common response variable in BEF studies.

This study focused on the production of stem biomass in monocultures vs. polycultures of forest trees. Experimental communities of young tree species were planted with orthogonal gradients of species richness and functional richness, allowing the effects of species number and trait diversity to be disentangled. Complementarity in tree canopy structure in these communities may be an important predictor of overyielding in stem biomass. Complementarity among tree crowns (that is, the extent to which they fit together spatially without overlapping, see Fig below) should reflect the ability of a set of species to maximize the efficiency of light usage as it hits the canopy. Such variation in crown canopy shapes among species could lead to a positive effect of having multiple species present in a community. 

Example of crown complementarity.
From Williams et al. 2017.

To test this, the authors estimated crown architecture for each species using traits that reflect crown shape and size. These measures were used to predict the spatial complementarity expected with different combinations of tree species. In addition, a single integrative trait – maximum growth rate – was measured for each species. The authors hypothesized that the variation in growth rate of species in a community would be associated with variation in crown heights and so also a good predictor of overyielding.

They found that crown complementarity occurred in nearly all of the experimental polycultures and on average was 29% greater in mixtures than monocultures. Controlling for the number of species, communities with greater variation in growth rate did in fact have greater crown complementarity, as predicted. Further, higher levels of crown complementarity were strongly associated (R2~0.6) with stem biomass overyielding.

Fig 2&3 from Williams et al (2017). For experimental communities:
a) the relationship between crown complementarity and variation in growth rate.
b) the relationship between crown complementarity and stem biomass overyielding.

These results provide a clear potential mechanism for a positive effect of biodiversity (particularly trait-based variation) in similar forests. (As they state, "We posit that crown complementarity is an important mechanism that may contribute to diversity-enhanced productivity in forests"). Given the importance of the sun as a limiting resource in forests, the finding that mixing species that combining shade intolerant and shade tolerant strategies are more productive (the authors note that "growth rate aligns with shade tolerance and traits indicative of a tree’s resource strategy") is not necessarily surprising. It fits within existing forestry models and practices for mixed stands. This is a reminder that we already understand many of the basic components of positive (and neutral and negative) diversity-functioning relationships. The good news is that ecology has accumulated a large body of literature on the components of overyielding (limiting resources, niche partitioning, evolution of alternate adaptive strategies, constraints on these, the strength of competition, etc). From the literature, we can identify the strongest mechanisms of niche partitioning and identify the contexts in which these are likely to be relevant. For example, sun in forests and canopy complementarity, or water limitation in grasslands and so root complementarity might be a good focal trait. 

Archiving the genomes of all species

There is so much bad news about global biodiversity, that it is nice to hear about new undertakings and approaches. One of these is the 'Earth BioGenome Project' which proposes to sequence the genomes of the entirety of life on earth. Given that sequencing services have never been more affordable and more available to scientists, without question, though ambitious this is a feasible undertaking. Still, with perhaps 9 million eukaryotes on the planet, a rough prediction suggests it could take 10 years and several billion dollars to achieve.

The cost suggests a certain agony of choice - what is the best use of that amount of money (in the dream world where money can be freely moved between projects)? Direct application to conservation and management activities, or a catalog of diversity which may be the only way to save some of these species? 

Leonard Eisenberg's tree of life (https://www.evogeneao.com).

The pessimistic and optimistic view of BEF experiments?

The question of the value of biodiversity-ecosystem function (BEF) experiments—their results, their relevancy—has become a heated one in the literature. An extended argument over the last few years has debated the assumption that local biodiversity is in fact in decline (e.g. Vellend et al. 2013; Dornelas et al. 2014; Gonazalez et al. 2016). If biodiversity isn't disappearing from local communities, the logical conclusion would be that experiments focussed on the local impacts of biodiversity loss are less relevant.

Two papers in the Journal of Vegetation Science (Wardle 2016 and Eisenhauer et al. 2016) continue this discussion regarding the value of BEF experiments for understanding biodiversity loss in natural ecosystems. From reading both papers, it seems as though broadly speaking, the authors agree on several key points: that results from biodiversity-ecosystem functioning experiments don’t always match observations about species loss and functioning in nature, and that nature is much more complex, context-dependent, and multidimensional than typical BEF experimental systems. (The question of whether local biodiversity is declining may be more contested between them). 

Biodiversity and ecosystem experiments typically involve randomly assembled plant communities containing either the full complement of species, or subsets containing different numbers of species. Communities containing lower numbers are meant to provide information about the loss of species diversity a system. Functions (often including, but not limited to, primary productivity or biomass) are eventually measured and analysed in relation to treatment diversity. Although some striking results have come out of these types of studies (e.g. Tilman and Downing 1996), they can vary a fair amount in their findings (Cardinale et al. 2012).

David Wardle’s argument is that BEF experiments differ a good deal from natural systems: in natural systems, BEF relationships can take different forms and explain relatively little variation, and so extrapolating from existing experiments seems uninformative. In nature, changes in diversity are driven by ecological processes (invasion, extinction) and experiments involving randomly assembled communities and randomly lost species do nothing to simulate these processes. Wardle seems to feel that the popularity of typical BEF experiments has come at the cost of more realistic experimental designs. This is something of a zero-sum argument, (although in some funding climates that may be true...). But it is true that big BEF experiments tend to be costly and take time and labour, meaning that there is an impetus to publish as much as possible from each one. Given BEF experiments have changed drastically in design once already, in response to criticisms about their inability to disentangle complementarity vs. portfolio effects, it seems they are not inflexible about design though.

Eisenhauer et al. agree in principle that current experiments frequently lack a realistic design, but suggest that there are plenty of other types of studies (looking at functional diversity or phylogenetic diversity, for example, or using random loss of species) being published as well. For them too, there is value in having multiple similar experiments: this allows metaanalysis and comparison aggregation, and will help to tease apart the important mechanisms eventually. Further, realism is difficult to obtain in the absence of a baseline for a “natural, untouched, complete system” from which to remove species.

The point that Eisenhauer et al. and Wardle appear to agree on most strongly is that real systems are complex, multi-dimensional and context-dependent. Making the leap from a BEF experiment with 20 plant species to the real world is inevitably difficult. Wardle sees this is a massive limitation, Eisenhauer et al. sees it as a strength. Inconsistencies between experiments and nature are information that highlight when context matters. By having controlled experiments in which you vary context (such as by manipulating both nutrient level and species richness), you can begin to identify mechanisms.

Perhaps this is the greatest problem with past BEF work, is that there is a tendency to oversimplify the interpretation of results – to conclude that ‘loss of diversity is bad’ but with less attention to ‘why’, 'where', or 'when’. The best way to do this depends on your view of how science should progress. 

Wardle, D. A. (2016), Do experiments exploring plant diversity–ecosystem functioning relationships inform how biodiversity loss impacts natural ecosystems?. Journal of Vegetation Science, 27: 646–653. doi: 10.1111/jvs.12399

Eisenhauer, N., Barnes, A. D., Cesarz, S., Craven, D., Ferlian, O., Gottschall, F., Hines, J., Sendek, A., Siebert, J., Thakur, M. P., Türke, M. (2016), Biodiversity–ecosystem function experiments reveal the mechanisms underlying the consequences of biodiversity change in real world ecosystems. Journal of Vegetation Science. doi: 10.1111/jvs.12435

Additional References:
Vellend, Mark, et al. "Global meta-analysis reveals no net change in local-scale plant biodiversity over time." Proceedings of the National Academy of Sciences 110.48 (2013): 19456-19459.

Dornelas, Maria, et al. "Assemblage time series reveal biodiversity change but not systematic loss." Science 344.6181 (2014): 296-299.

Gonzalez, Andrew, et al. "Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity." Ecology (2016).

Tilman, David, and John A. Downing. "Biodiversity and stability in grasslands." Ecosystem Management. Springer New York, 1996. 3-7.

Cardinale, Bradley J., et al. "Biodiversity loss and its impact on humanity."Nature 486.7401 (2012): 59-67.

Is there a limit to how many species can the earth hold?

Counting species (bird lists, plant guides) is as old as ecology itself. And yet surprisingly, there are still different opinions on how many species the planet holds, and even, whether there are limits on how many species it can have. If the number of species has ecological limits, the assumptions ecologists often make – that species pools are limited and knowable, dynamics can reach equilibrium, competition should usually be important – would be stronger. Things would be more predictable. 

But is the production of diversity self-limited? There isn’t consensus but two recent articles in the American Naturalist (continuing a debate at the American Society of Naturalists meeting) provide some excellent debate of this question.

The debate is whether the majority of variation in continental-scale species richness is regulated by diversity-dependent feedbacks. In these papers, Dan Rabosky and Allen Hurlburt argue that species richness has ecological limits, while Luke Harmon and Susan Harrison take the contrary position, that species richness is dynamic. First, to define some terms: here, species richness is being considered at the largest spatial scale (e.g. terrestrial plants at the continental scale) so that dispersal limitation should be comparatively unimportant (because diversity changes are mostly driven by in situ speciation).

The crux of the Rabosky & Hurlburt argument is established in the Ecological Limits Hypothesis (ELH), which states that species richness will reach a dynamic (i.e. stochastic) equilibrium, where equilibrium richness reflects density dependence in speciation and/or extinction rates. Speciation and extinction rates are ultimately limited by total resource availability for the continent. Therefore variance in richness through time and between places should be driven these ecological limits, and richness should be predictable.

From Rabosky & Hurlburt 2015 - the Ecological Limit Hypothesis.

The evidence presented for the ELH comes from phylogenies and macroevolutionary models, the fossil record, and macroecological observations. First, there are well known patterns between species richness and energy, productivity, or habitat area, and these span multiple regions and groups of species (e.g. Jetz and Fine 2012). Further, Rabosky & Hurlburt argue that geological records suggest that changes in diversity are not unbounded or exponential, but instead rise and fall, correcting toward some equilibrium. Molecular phylogenies are often evaluated by looking at speciation rates over time, and the authors suggest that these frequently show declines, where speciation declines during adaptive radiations. One prediction that arises from the ELH is that perturbations will be followed by particular responses: “negative perturbations—mass extinctions, in particular—should lead to diversity recoveries. Second, positive perturbations—increases in the resource base available to a biota—predict increases in species richness to stable but greater equilibrial levels”.

The rebuttal article from Harmon & Harrison takes a strong and contrasting view, although it focuses mostly on poking holes into Rabosky & Hurlburt’s arguments, rather than laying out a competing hypothesis. If Rabosky & Hurlburt focused on evidence over huge evolutionary scales and spatial expanses, the Harmon & Harrison response has a particular interest in the temporal and spatial scales of interest to community ecologists (local, present day) and how these seem to disagree with Rabosky & Hurlburt's hypothesis.

First, Harmon & Harrison argue that that the macroevolutionary evidence (molecular phylogenies, fossil data) is not nearly so convincing as Rabosky & Hurlburt suggest. There are important limits to its utility resulting from issues of ambiguity in interpretation and methodological limitations. In addition, for most of the patterns Rabosky & Hurlburt highlight, there are other papers concluding that the pattern was not present in their data. With reference to the lack of relationship between clade age and diversity: “A common interpretation of these results is that a lack of a relationship between age and diversity is evidence for ecological limits.... However… this pattern is far from ubiquitous in real data and is compatible with other explanations”. They also take issue with the tendency for hand-wave-y interpretations of patterns in such data, and emphasize the need for better statistical analyses and consideration of alternate models. Fossil data has obvious limitations as well (hence the field of taphonomy), including the fact that fossils are rarely classified to the species-level, which means they do not represent species richness, but rather lineage richness.

But Harmon & Harrison's real disagreement is based on their view that ecological evidence from local communities does not at all suggest ecological limits. Energy-richness correlations, although common, may have alternative explanations: the tropics may have higher diversification rates for other reasons, or niche conservation means that more species niches suited to the tropics, confounding energy-diversity relationships. Further, local communities do not regularly show a positive energy-diversity relationship. In particular, Harmon & Harrison suggest that the logic from the ELH, if followed, predicts that if species richness is ultimately tied to the availability of energy, then competition should necessarily be very important in most ecological communities. They cite a stat from the invasion of California flora in which alpha diversity has risen by more than 1000 invasive species, with only 28 native extinctions (as of 2002), suggesting that local (or even regional) communities are not full. 

To this, Rabosky & Hurlburt rejoins that invasion is about dispersal changes, and not resources. Further, they believe that large evolutionary scales are most useful as evidence for the ELH, since they are most likely to show zero sum game, rather than temporary dynamics, and since confounding factors should become minimized.

The debate left me feeling a little unsatisfied (since expecting the authors solve the problem is a bit unreasonable), in part because the authors are really arguing from different scales and approaches. And both sides are clearly right in some cases (and in others, perhaps, clearly overreaching). And of course, proving whether or not there is an ecological limit on diversity is a rather difficult thing. When Harmon and Harrison argue that the ELH, which assumes that richness approaches some equilibrium value but varies about it in a stochastic fashion, isn’t parsimonious, they’re wrong – ecological processes are innately stochastic and it hardly seem un-parsimonious to assume as much. But they’re right that this view makes testing and model fitting very difficult since having high replication and good quality data is necessary (to capture accurately a distribution, rather than single value). Given the variety of issues with data representing diversification over evolutionary time, and frequently an inability to capture extinction rates with evolutionary data, having quality, replicated tests of the ELH is difficult.

On the other hand, at local scales over ecological time, observations may be less relevant. It’s not clear how to reconcile statements about saturation (or lack thereof) of local communities with richness at continental scales. Rabosky & Hurlburt suggest that local assemblages can be dynamic in diversity as long as there is a zero sum across all communities and through time. But a connection between continental scales and local scales is innate, and understanding how diversity relates over multiple spatial scales is an area of ecological research we need to continue to develop.

Given there are no easy tests of this sort of question (though bacterial microcosm provide some interesting results), we have been forced to draw conclusions based on weak tests and weak evidence. But ecologists do this because this is a truly important question, with huge implications across ecology and evolution. Ecological and evolutionary models make assumptions that implicitly or explicitly about carrying capacity, about determinants of rates of speciation and extinction, about invasion, about why global diversity changes, and these need to be confirmed. Further, if there is a strong ecological feedback of diversity, one of the most important implications is that major perturbations such as extinctions should be followed by major recoveries. In the Anthropocene, that’s an important implication. 

References:

Species Richness at Continental Scales Is Dominated by Ecological Limits. Daniel L. Rabosky, Allen H. Hurlbert. The American Naturalist, Vol. 185, No. 5 (May 2015), pp. 572-583.

Species Diversity Is Dynamic and Unbounded at Local and Continental Scales. Luke J. Harmon, Susan Harrison. The American Naturalist, Vol. 185, No. 5 (May 2015), pp. 584-593.

#ibs2015 – Confronting uncertainty, biases and the unknown

The 2015 meeting of the International Biogeography Society just came to an end, and even for someone who wouldn’t traditionally consider themselves a ‘biogeographer’ there were many interesting topics and talks to see.

The focus of most talks was on biological patterns over space and/or time (or ‘deep time’, which is a fun phrase to throw around), and the talks emphasized how sophisticated statistical methodologies for such questions have become. The extent and complexity of approaches for making inferences from limited existing information, be it phylogenetic, distributional, or fossil and pollen records, is pretty amazing.

Such complicated inference needn't and shouldn't come at the cost of careful scientific work, and must include recognition of uncertainty and biases. The final sessions of the conference acted as an excellent (and at times provocative) reminder of this. For example, Joaquin Hortal advocated the development of ‘maps of ignorance’, which instead of showing the typical distributions of known information, highlight where information is missing and new sampling should be emphasized. Not only is information sometimes missing, but its value degrades over space and time. The value of a sample declines the further away you get from that site or the more different the spatial scale; samples over 50 years old may not represent current conditions any more. Predictions should consider or even incorporate this uncertainty.

Catherine Graham, David Nipperess, and Jon Chase all gave talks similarly emphasizing how fundamental consideration of scale and extent is. This is as true for phylogenetic community analysis (Graham, what extent or size of tree should be considered for analyses of community phylogenetics?); for rarefaction of phylogenetic diversity (Nipperess); or for measures of beta-diversity (Chase). Without this context, we are likely to be misunderstanding our results.

Finally, David Currie gave a damning critique of macroecology. Unfortunately, he said, macroecology seems to be a field where hypothesis testing is rare and conclusions are drawn based on spurious correlations with little explanatory and even less predictive ability. For example, why has the study of latitudinal gradients in richness progressed little beyond a list of possible correlates after more than 30 years of attention? Though Currie was focused on his own field, his comments were relevant to many ecological approaches. Currie expressed concerns about areas where scientific methods were being given short shift. In particular, he noted a lack of appropriate hypothesis testing and strong inference. Instead there is a tendency for studies to look for evidence in support of a hypothesis of interest, rather than attempting to falsify a hypothesis. Supporting evidence, sadly, does not actually increase the probability that a hypothesis is true, since the evidence could equally support some other, currently unconsidered, hypothesis. Further, correlations between variables of interest are at best a weak test of a hypothesis. The most important suggestions were that macroecologists and others should be testing the predictive ability of their hypotheses on new data sets: model fitting, in his opinion, is too often confused with model testing.

Could today’s oil rigs be tomorrow’s biodiversity hotspots?

*Guest post by Bryan Flood -one of several posts selected from the graduate EES3001 Scientific Literacy course at University of Toronto-Scarborough.

New research by Jeremy Claisse and colleagues at Occidental College in Los Angles have discovered that secondary fish production at oil and gas platforms off the coast of California is up to an order of magnitude higher than other marine ecosystems. This includes reefs and estuaries, normally considered some of the most productive ecosystems on the planet.

Photo from: US Bureau of Ocean Energy Management - http://www.data.boem.gov/homepg/data_center/other/imagecate/imageview.asp?ID=292

The authors measured the total productivity at oil and gas platforms and divided by the platform’s footprint to get a per-square-metre productivity. Herein lies the secret: The authors attribute these phenomenal productivities to the large hardscape (physical surfaces of the rigs) to seafloor ratio.

Having a structure that spans the total water column creates a range of habitats for a diverse variety of species and life stages, as well as creating a complex structure with large surface area which translates directly into habitat. This habitat attracts many species including rockfish larvae, invertebrates and planktonic food resources. These form the base of the food web, subsequently attracting adult fish and other organisms.

These results have important implications for the future of the more than 7500 oil and gas platforms around the world that will need to be decommissioned at the end of their service life. Should they be dismantled, or left as artificial reefs? Should future platforms and wind turbines be designed with an afterlife as an artificial reef in mind? Could these structures one day dot the seas with aquatic metropolises?

Claisse, J., Pondella, D., Love, M., Zahn, L., Williams, C., Williams, J., & Bull, A. (2014). Oil platforms off California are among the most productive marine fish habitats globally Proceedings of the National Academy of Sciences, 111 (43), 15462-15467 DOI: 10.1073/pnas.1411477111

Do green roofs enhance urban conservation?

Green roofs are now commonly included in the design of new public and private infrastructure, bolstered by energy savings, environmental recognition and certification, bylaw compliance, and in some cases tax or other direct monetary incentives (e.g., here).  While green roofs clearly provide local environmental benefits, such as reduced albedo (sunlight reflectance), storm water retention, CO₂ sequestration, etc., green roof proponents also frequently cite biodiversity and conservation enhancement as a benefit. This last claim has not been broadly tested, but existing data was assessed by Nicholas Williams and colleagues in a recent article published in the Journal of Applied Ecology.

Williams and colleagues compiled all available literature on biodiversity and conservation value of green roofs and they explicitly tested six hypotheses: 1) Green roofs support higher diversity and abundance compared to traditional roofs; 2) Green roofs support comparable diversity and composition to ground habitat; 3) Green roofs using native species support greater diversity than traditional green roofs; 4) Green roofs aid in rare species conservation; 5) Green roofs replicate natural communities; and 6) Green roofs facilitate organism movement through urban areas.

Photo by: Marc Cadotte

What is surprising is that given the abundance of papers on green roofs in ecology and environmental journals, very few quantitatively assessed some of these hypotheses. What is clear is that green roofs support greater diversity and abundance compared to non-green roofs, but we know very little about how green roofs compare to other remnant urban habitats in terms of species diversity, ecological processes, or rare species. Further, while some regions are starting to require that green roofs try to maximize native biodiversity, there are relatively few comparisons, but those that exist reveal substantial benefits for biodiverse green roofs.

How well green roofs replicate ground or natural communities is an important question, with insufficient evidence. It is important because, according to the authors, there is some movement to use green roofs to offset lost habitat elsewhere. This could represent an important policy shift, and one that may ultimately lead to lost habitats being replaced with lower quality ones. This is a policy direction that simply requires more science.

There is some evidence that green roofs, if designed correctly, could aid in rare species conservation. However, green roofs, which by definition are small patches in an inhospitable environment, may assist rare species management in only a few cases. The authors caution that enthusiasm for using green roofs to assist with rare species management needs to be tempered by designs that are biologically and ecologically meaningful to target species. They cite an example where green roofs in San Francisco were designed with a plant that is an important food source for an endangered butterfly, Bay Checkerspot, which currently persists in a few fragmented populations. The problem was that the maximum dispersal distance of the butterfly is about 5 km, and there are no populations within 15 km of the city. These green roofs have the potential to aid in rare species conservation, but it needs to be coupled with additional management activities, such as physically introducing the butterfly to the green roofs.

Overall, green do provide important environmental and ecological benefits in urban settings. Currently, very few studies document the ways in which green roofs provide ecological processes and services, enhance biodiversity, replicate other ground level habitats, or aid in biodiversity conservation. As the prevalence of green roofs increases, we will need scientifically valid ecological understanding of green roof benefits to better engage with municipal managers and affect policy.

Williams, N., Lundholm, J., & MacIvor, J. (2014). Do green roofs help urban biodiversity conservation? Journal of Applied Ecology DOI: 10.1111/1365-2664.12333

Data merging: are we moving forward or dealing with Frankenstein's monster

I’m sitting in the Sydney airport waiting for my delayed flight –which gives me some time to ruminate about the mini-conference I am leaving. The conference, hosted by the Centre for Biodiversity Analysis (CBA) and CSIRO in Australia, on "Understanding biodiversity dynamics using diverse data sources", brought together several fascinating thinkers working on disparate areas including ecology, macroecology, evolution, genomics, and computer science. The goal of the conference was to see if merging different forms of data could lead to greater insights into biodiversity patterns and processes. 

Happy integration

On the surface, it seems uncontroversial to say that bringing together different forms of data really does promote new insights into nature. However, this only really works if the data we combine meaningfully complement one another. When researchers bring together data, there are under-appreciated risks, and the resulting effort could result in trying to combine data that make weird bedfellows.

Weird bedfellows

The risks include data that mismatch in the scale of observation, resulting in meaningful variation being missed. Data are often generated according to certain models with specific assumptions, and these data-generation steps can be misunderstood by end-users, resulting in inappropriate uses of data. Further, different data may be combined in standard statistical models, but the linkages between data types is much more subtle and nuanced, requiring alternative models.

Why these are issues stems from the fact that researchers now have an unprecedented access to numerous large data sets. Whether these are large trait data sets, spatial locations, spatial environmental data, genomes, or historical data, they are all built with specific underlying uses, limitations and assumptions.  

Regardless of these issues of concern, the opportunity and power to address new questions is greatly enhanced by multiple types of data. One thing I gained from this meeting is that there is a new world of biodiversity analysis and understanding emerging by smart people doing smart things with multiple data. We will soon live in a world where the data and analytical tools allow research to truly combine multiple processes to predict species' distributions, or to move from evolutionary events in deep history to modern day ecological patterns.