Post at Oikos + why do papers take so long?

This is mostly a shameless cross-post to a blog post I wrote for the Oikos blog. It's about an upcoming paper in Oikos that asks whether beta-diversity null deviation measures, which originated in papers like Chase 2010 and Chase et al. 2011, can be interpreted and applied as a measure of community assembly. These measures were originally used as null models for beta-diversity (i.e. to control for the effects of alpha diversity, etc), but increasingly in the literature they are used to indicate niche vs. neutral assembly processes. For anyone interested, the post is at the Oikos blog: http://www.oikosjournal.org/blog/v-diversity-metacommunities.

What I found most amusing, or sad, depending on your perspective was that I wrote a blog post about some of the original conversations I had with co-authors about this subject. I looked it up the other day and was shocked that the post was from 2013 (http://evol-eco.blogspot.com/2013/11/community-structure-what-are-we-missing.html). It's amazing how long the process of idea to final form actually takes. (No one phase took that long either - just idea + writing + coauthor edits + rewriting + submit + revise + coauthors + revise = long time...)

Disagreeing about ecology: how debate advances science

• Kraft N.J.B. et al. 2011. “Disentangling the Drivers of β-Diversity Along Latitudinal and Elevational Gradients” Science. Vol. 333:6050 pp.1755-1758
• Qian. H. et al. 2012. Comment on “Disentangling the Drivers of β Diversity Along Latitudinal and Elevational Gradients”. Science 30:1573.
• Tuomisto, H. and Ruokolainen, K. 2012. Comment on“Disentangling the Drivers of β Diversity Along Latitudinal and Elevational Gradients”. Science 30:1573.
• Kraft N.J.B. et al. 2012. Response to Comments on“Disentangling the Drivers of β Diversity Along Latitudinal and Elevational Gradients”. Science 30: 1573.

A good scientific debate makes for excellent spectator sport (although it’s probably less fun for the participants). Many of the best ecological debates are now classics of the literature—Diamond vs. Simerberloff, Lawton vs. Simberloff, Hubbell vs. many—and these historical debates influence present day ecology. Interestingly, debates in ecology seem to revolve around two particular issues: whether the data is appropriate and whether the methods are adequate to draw conclusions about a particular process.

As an example, there’s a typical ecological debate occurring in Science over Kraft et al.’s “Disentangling the drivers of β-diversity along latitudinal and elevational gradients”. In this paper, the authors reevaluate the mechanisms that drive changes in species identity along latitudinal and elevation gradients using a null model. Although β-diversity may vary along biogeographical gradients as a result of processes such as dispersal limitation, range size, and habitat filtering, total (γ) diversity also varies along these gradients (we know that richness is generally higher in the tropics and the lowlands). Since this suggests that γ- and β-diversity aren’t independent, it may be that changes in γ-diversity need to be accounted for as an explanation for changes in β-diversity (Chase 2011). When Kraft et al. controlled for γ-diversity using a null model, they found that the magnitude of β-diversity did not vary along latitudinal or elevational gradients. They stated that this means: “there may be no need to invoke differences in the mechanisms of community assembly in temperate versus tropical systems to explain these global-scale patterns of β-diversity.”

This conclusion is in contrast to multiple papers that have suggested that tropical communities are somehow structured differently from temperate communities. Such work has been far from conclusive, however, finding evidence for everything from stochastic assembly to microhabitat-driven assembly in tropical regions. However, given the strong conclusion from the Kraft et al. paper, it’s not surprising that there were several responses from other researchers of β-diversity (Tuomisto and Ruokolainen and Qian et al.). It’s also not surprising that the points raised in these responses are fairly typical for debates in community ecology, calling into question the suitability of the data, the appropriateness of the spatial scale for capturing the processes of interest, and the question of whether the methods are correct. The debate is as much about the fundamental questions of how we define and measure β-diversity as it is about the particulars of the Kraft et al. article.

For example, both Tuomisto and Ruokolainen and Qian et al. questioned the sampling design of the data, as to whether there was too much within-plot variation (Tuomisto and Ruokolainen) or, alternately, too little between-plot variation (Qian et al.) to correctly capture the amount of β-diversity. Tuomisto and Ruokolainen further suggested that the plots used in the original study undersample local (α) diversity and therefore overestimate the differences between plots. Both sets of authors suggest that inappropriate sampling would make it difficult to generalize Kraft et al.’s results to other studies of β-diversity. Kraft et al.’s response was that although plots are placed to minimize among-plot environmental variation, this does not make them inappropriate to test for finer scale evidence of environmental processes, and that β-diversity still varies markedly between plots. However, given that this debate - about whether there is a “best” spatial scale at which to examine the ecological causes of β-diversity and a “best” way to sample to capture variation among communities – is occurring among experienced β-diversity researchers suggests that these are still fuzzy areas.

Another aspect of this debate relates to the ongoing discussion about the appropriate definition and calculation of β-diversity (Tuomisto 2010). The most traditional methods define β-diversity as a multiplicative or additive function of α- and γ-diversity, and Kraft et al. argue that as a result β-diversity is not independent of those variables. To account for this fact, Kraft et al. use a null model that incorporates γ-diversity, to predict β-diversity under random or stochastic assembly. However, Tuomisto and Ruokolainen argue that the measure of β-diversity used (β_P = 1 – α/γ) is such that γ-diversity can vary without affecting β-diversity, provided alpha-diversity is also free to vary. However, Kraft et al. dispute this, suggesting that perfectly scaled changes in both γ- and α-diversity, such that β-diversity remains unchanged, represent a special case that does not appear in their data set.

Of course, other points were discussed among the authors. Qian et al. disagreed with the use of latitudinal gradients, noting that the ecological “meaning” of a given latitude is rather vague. However, given that the authors admit their site data is likely to capture small-scale variation in β-diversity, it seems that trying to relate their results to large-scale latitudinal or elevational gradients is a greater issue.

Kraft et al. suggested in their response that many of the criticisms were misunderstandings of the methods and findings of the original paper. You might more correctly say that disagreements like this capture important weaknesses or ambiguities in current understanding and theory. It’s true that at their worst, debates create conflict and that since responses are rarely peer-reviewed to the same extent the original publication is, too much weight may be given to meritless counter-arguments. However, good debate should drive progress, force researchers to reevaluate their assumptions, and ultimately hold science accountable. And for that reason it should be encouraged.

**I should note that this post is specifically meant in relation to debate among researchers, not to situations where scientists are in agreement and the debate is occurring in the public sphere.