Thursday, November 14, 2013

How many traits make a plant? How dimensionality simplifies plant community ecology.

Daniel C. Laughlin. 2013. The intrinsic dimensionality of plant traits and its relevance to community assembly. Journal of Ecology. Accepted manuscript online: 4 NOV. DOI: 10.1111/1365-2745.12187

Community ecology is difficult in part because it is so multi-dimensional: communities include possibly hundreds of species present, and in addition the niches of each of those species are multi-dimensional. Functional or trait-based approaches to ecology in particular have been presented as a solution to this problem, since fewer traits (compared to the number of species) may be needed to capture or predict a community’s dynamics. But even functional ecology is multi-dimensional, and many traits are necessary to truly understand a given species or community. The question, when measuring traits to delineate a community is: how many traits are necessary to capture species’ responses to their biotic and/or abiotic environment? Too few and you limit your understanding, too many and your workload becomes unfeasible.

Plant communities in particular have been approached using a functional framework (they don't move, so trait measurements aren't so difficult), but the number and types of traits that are usually measured vary from study to study. Plant ecologists have defined functional groups for plants which are ecologically similar, identified particular (“functional”) traits as being important, including SLA, seed mass, or height, or taken a "more is more" approach to measurements. There are even approaches that capture several dimensions by identifying important axes (leaf-height-seed strategy, etc.). Which of these approaches is best is not clear. In a new review, Daniel Laughlin rather ambitiously attempts to answer how many (and which) traits plant ecologists should consider. He asks whether the multi-dimensional nature of ecological systems is a curse (there is too much complexity for us to ever capture), or a blessing (is there a limit on how much complexity actually matters for understanding these systems)? Can dimensionality help plant ecologists determine the number of traits they need to measure? 
From Laughlin 2013. The various trait axes (related to plant organs) important for plant function.
Laughlin suggests that an optimal approach to dimensionality should consider each plant organ (root, leaves, height, figure above). Many of the traits regularly measured are correlated (for example, specific leaf area, leaf dry matter content, lifespan, mass-based maximum rate of photosynthesis, dark respiration rates, leaf nitrogen concentration, leaf phosphorus concentration are all interrelated), and so potentially redundant sources of information. However, there are measurements in the same organ that may provide additional information – leaf surface area provides different information than measures of the leaf economic spectrum – and so the solution is not simply measuring fewer traits per organ. Despite redundancy in the traits plant ecologists measure, it is important to recognize that dimensionality is very high in plant communities. Statistical methods are useful for reducing dimensionality (for example, principle coordinate analysis), but even when applied, Laughlin implies that authors often over-reduce trait data by retaining to only a few axes of information.

Using 3 very large plant species-trait datasets (with 16-67(!) trait measures), Laughlin applies a variety of statistical methods to explore effective dimensionality reduction. He then estimates the intrinsic dimensionality (i.e. the number of dimensions necessary to capture the majority of the information in community structure) for the three datasets (figure below). The results were surprisingly consistent for each data set – even when 67 possible plant traits were available, the median intrinsic number of dimensions was only 4-6. While this is a reasonably low number, it's worth noting that the number of dimensions analyzed in the original papers using those datasets were too low (2-3 only).
From Laughlin 2013. The intrinsic number of traits/dimensions
necessary to capture variation in community structure.
For Laughlin, this result shows that dimensionality is a blessing, not a curse. After all, it should allow ecologists to limit the number of trait measures they need to make, provided they choose those traits wisely. Once the number of traits measured exceeds 8, there appears to be diminishing returns. The caveat is that the traits that are important to measure might differ between ecosystems – what matters in a desert is different than what matters in a rainforest. As always, knowing your system is incredibly important. Regardless, the review ends on a highly optimistic note – that complexity and multi-dimensionality of plant communities might not limit us as much as we fear. And perhaps less work is necessary for your next experiment.


Anonymous said...

Cool stuff. Reminds me a bit of this work in evolutionary biology:

Anonymous said...

I haven't read the paper (although I intend to), but my initial thought is that dimensionality estimates will be sample-size dependent. Many measures of diversity are sample-size dependent, which is why we need rarefaction and other related tools. Thanks again for your inspiring reports of new research.