Reinterpreting phylogenetic patterns in communities

Examining the phylogenetic structure of a community in order to understand patterns of community assembly has become an increasingly popular approach. A quick web search of “community”, “phylogenetics”, and “ecology” finds several hundred papers, most written in the last ten years.

Eco-phylogeneticists examine how patterns of evolutionary relatedness within communities may reflect the processes structuring those communities. In particular, a commonly tested hypothesis is the competition-relatedness hypothesis, which suggests that more closely-related species having more similar niches and therefore stronger competitive interactions, making coexistence between them less likely. As a result, if competition is important, communities may exhibit phylogenetic overdispersion, with species being less related on average than if drawn randomly from the regional species pool. The contrasting pattern, phylogenetic clustering, where species tend to be more closely related than expected, is often interpreted as being the result of strong environmental filtering, such that only a closely related group of species, best adapted to that environment, surviving in the community.

Evidence for the competition-relatedness hypothesis has been mixed, and since most tests of this hypothesis focus on patterns in observed data, conclusions about the underlying mechanism driving community phylogenetic patterns are rarely testable, and yet widely made.

In Mayfield and Levine (2010, Ecology Letters), the authors critique the current ecological justification for the competition-relatedness hypothesis, noting that it does not agree with a more current view of the processes driving species coexistence. As established by Chesson (2000, Annual Review of Ecology and Systematics), coexistence can involve both stabilizing forces (niche differences between species), and equalizing forces (fitness differences between species). In a simplistic example, plants using different soil types (niche differences) may coexist, while plants with similar high growth rates may exclude those species with lower growth rates (fitness differences). The final community should reflect the interplay of both these processes.

The implication of this view of species coexistence is that there is no preconceived phylogenetic pattern which should reflect competition: if species with the highest heights are competitively superior and exclude other species (coexistence driven by fitness differences), and height is a phylogenetically conserved trait, the community will appear to be phylogenetically clustered. Traditionally, a clustered pattern would not be considered to indicate the effects of competition. In fact, Mayfield and Levine show that the expected phylogenetic pattern depends entirely on whether niche and/or fitness differences are important and/or related to phylogenetic distance.

This suggest that conclusions in past studies may need to be reinterpreted. It also adds to the list of assumptions about evolutionary relatedness and ecological function which need to be tested: for example, how do niche and fitness differences tend to change through time? Do they tend to be conserved among closely related species? Does one or the other tend to dominate as a driver of coexistence in different systems? If nothing else, we need to be careful about making generalizations which don’t account for the differing evolutionary history, geographical location, and ecological setting that communities experience, when interpreting observed patterns in those communities.

Organic farming and natural enemy evenness

The basic reality of agricultural activity is that it reduces biological diversity, and these reductions in diversity potentially impact ecosystem services. But do some agricultural practices impact these services less than others? In a recent paper in Nature by David Crowder and colleagues, the question of how organic versus conventional farming affects predator and herbivore pathogen diversity and how this cascades to pest suppression. They show through a meta-analysis, that organic farms tend to support greater natural enemy evenness, and they hypothesize that greater evenness of enemies should better control pest populations, resulting in larger, more productive plants.

Picture from wikipedia

This result in itself is interesting, but they also carried out an elegant enclosure experiment where they manipulate the evenness of insect predators and pathogens and measure potato plant size. They found that even communities had the lowest herbivore densities and saw the greatest increases in plant biomass. Conversely, very uneven communities, typical of conventional farms, had the largest pest populations resulting in lower plant biomass accumulation.

While, multiple farming strategies are needed for adequate agricultural production, there are strong arguments for organic farms to be a important part of agricultural practice. These results show that organic farms have cascading effects on pest predators and pathogens and show that enemy evenness, as opposed to richness, has important ecosystem service consequences. To quote myself, evenness is a critical component of biodiversity, and much research has emphasized species richness, maybe at the detriment of studying evenness.

Crowder, D., Northfield, T., Strand, M., & Snyder, W. (2010). Organic agriculture promotes evenness and natural pest control Nature, 466 (7302), 109-112 DOI: 10.1038/nature09183

New Carnival of Evolution

Check out the July edition of the Carnival of Evolution written by Hannah Waters at Culturing Science.

Happy Year of Biodiversity

It’s ironic that during the International Year of Biodiversity, the US is experiencing an environmental disaster on a massive scale. Unfortunately, this disaster is just another failure in environmental protection, part of a long series of failures which seem to characterize this Year of Biodiversity. Even as the political will behind the 2010 biodiversity targets seems to have waned (and most indicators suggest that declines in diversity are unchecked), evidence continues to mount for the functional value of biological diversity.

This week’s issue of Nature features a couple of pieces focusing on biodiversity through a political or economic lens. Although the economic benefits and services provided by species-level diversity has been well illustrated, in “Population diversity and the portfolio effect in an exploited species”, Schindler et al. (Nature, 465, 609-612) new evidence that at even finer divisions than the species, diversity plays an important role. In this case, they find that genetic diversity at the population level is an additional and significant contributor to ecosystem stability. Schindler et al. examine the effects of hundreds of locally-adapted populations of sockeye salmon on the valuable salmon fishery in the Bristol Bay area of Alaska. They suggest that the portfolio effect (or the robustness of biodiversity to variable conditions – like a diverse financial portfolio) can function at the population level as well as the species level. High levels of intra-specific diversity can produce temporal variation among populations in response to environmental variability, resulting in catches that are more stable year-to-year, and making fishery closures less likely, a clear economic benefit.

Populations are declining at an even faster rate than species themselves: the more we understand the importance of conserving diversity at multiple biological scales (ecosystem, species, population, even the individual?), the more complicated and onerous the task of conserving diversity becomes.

In the same issue of Nature is an editorial on the possibility of an IPCC-like panel for biodiversity. At this very moment (give or take a few time zones), government representatives from all over the world are deciding whether or not to create this panel. So far, they have a catchy name for it, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), which hopefully hasn’t been written in stone. But they also have a strong recognition of the inextricable links between biodiversity, ecosystem services and human wellbeing – links that are highlighted in the Schindler et al. article. Furthermore, an explicit goal of IPBES is to address the currently tangled state of biodiversity organizations, conventions and programs by forming a unified front of sound biodiversity policy and science. The Convention on Biological Diversity had set a target of halting biodiversity loss by 2010 and we have failed spectacularly. Is IPBES the solution?

Wanted: an IPCC for biodiversity. Nature, 465, 525-525

Schindler, D.E., Hilborn, R., Chasco, B., Boatright, C.P., Quinn, T.P., Rogers, L.A. & Webster, M.S. Population diversity and the portfolio effect in an exploited species. Nature, 465, 609-612

By Nick Mirotchnick and Caroline Tucker

Another reason why a new publishing model is needed...

The finances and ethics of scientific publishing are complex, and there is an inherent tension between commercial publishers and academics and their institutions. On the one hand, we as scientists are (most often) using public money to carry out research, usually in the public interest, and then we typically publish in for-profit journals that restrict public access to our publications. Authors seldom see any of the financial return from publisher profits. On the other hand, publishers provide a level of distribution and visibility for our work, which individual authors could not match. In previous posts I have discussed Open Access publications, but there is another reason to consider other publication models. Recently Nature Publishing Group notified the University of California system of an impending 400% increase in the cost for their publications. The UC administration has responded with an announced plan to boycott NPG publications. The announcement rightly points out a 400% increase is not feasible given the current plight of library budgets, especially in California, and that scientists in the UC system disproportionately contribute to publishing, reviewing and editing NPG publications and thus are the engine for NPG profits. (See a nice story about the boycott in The Chronicle of Higher Education)

This is just the latest symptom of the growing tension between publishing and academia, and is a stark reminder that other publishing models need to actively supported. Perhaps the UC system could invest in open access publishers in lieu of NPGs outrageous costs? Something has to give, and perhaps the UC boycott will remind libraries that they hold the purse strings and could be the greatest driving force for change.

Experimental test of Darwin's naturalization hypothesis

Among the numerous and still informative ecological predictions made by Darwin, one posits that when species are introduced into regions where they were not formerly found, the most successful tend to not have close relatives already occupying the region. This is known as Darwin's Naturalization Hypothesis, and his logic was that among close relatives, where ecological requirements should be most similar, the struggle for existence is most severe. Thus the modern formulation is that invader success is influenced by the amount of time since two species shared a common ancestor (usually called phylogenetic distance). Tests of this hypothesis have been primarily done on large species inventories, with results from different studies either supporting or refuting it. In a new study by Lin Jiang and colleagues published in the American Naturalist, they cleverly use bacteria with known relatedness to test this hypothesis.

They used four species of bacteria: Bacillus pumilus, B. cereus, Frigoribacterium sp. and Serratia marcescens as residents in every possible 1, 2, 3 and 4-species communities and invaded them with a subspecies of S. marcescens. What they found was that the invader density was highly significantly related to phylogenetic distance, so that the invader reached its greatest density when communities contained only distantly-related species.

Though these types of laboratory experiments are simplistic (I too use these systems), they offer insights into particular mechanisms, which may otherwise be difficult to detect in noisier systems.

Jiang, L., Tan, J., & Pu, Z. (2010). An Experimental Test of Darwin’s Naturalization Hypothesis The American Naturalist, 175 (4), 415-423 DOI: 10.1086/650720