Experimental community assembly: when do niche-assembly processes matter?

This post was contributed by Kristina Riemer who is a PhD candidate in Dr. Ethan White’s lab 

With the introduction of neutral theory in Hubbell (2001), ecologists began to discuss the relative importance of species identities, including traits, in ecological communities. The two papers that we discussed were intended to capture some of the experimental research that has been done on the importance of such niche-based processes on community assembly, which is unfortunately relatively rare. The first paper contains the results from laboratory-based experiments using protist microcosms, while the second paper presents results from experiments done in the field using grassland plants.

  • Jiang, L. and S.N. Patel. 2008. Community assembly in the presence of disturbance: microcosm experiment. Ecology 89:1931-1940. (pdf)
  • Fargione, J., C. Brown, and D. Tilman. 2003. Community assembly and invasion: an experimental test of neutral versus niche processes. PNAS 101:8916-8920. (pdf)

While the study organisms and experimental methods in these papers were very different, the research questions and results were similar. The authors in these papers were determining whether and when niche-assembly processes, as opposed to neutral processes, were important in their systems. Niche-assembly processes occur when the traits or differences between organisms are influential in the assembly of their communities. Jiang and Patel (2008) focused on how different levels of disturbance affected the influence of traits, while Fargione, Brown, and Tilman (2003) addressed if functional traits influenced the ability of new species to become established in a community.

Jiang and Patel (2008) introduced 10 species of protists, in stable groups of two species, to individual microcosms randomly. For each of five randomly chosen sequences, one group of two species was added each week for five weeks. In the control microcosms, all 10 species were added simultaneously. The species composition of each microcosm was then determined every week for the following six weeks. Additionally each sequence underwent three disturbance regimes: low, medium, and high. This disturbance was in the form of sonication of increasing percentage of the microcosm medium. Each sequence and disturbance regimes combination was replicated three times.

The authors determined that niche-assembly processes were more important in high disturbance regimes than in low. Microcosms that experienced high disturbance had communities that were more similar, which led to the conclusion by Jiang and Patel (2008) of less alternative stable states in these communities. They explained that this was likely due to the greater environmental filter created by disturbance, which filtered out those species that did not have traits that conferred disturbance resistance. Therefore, niche-assembly processes were important in the assembly of these communities. Conversely, communities with low disturbance levels had more variable species composition. Traits that provide advantages in disturbance were not as important in assembly of these communities as colonization history was. Therefore, neutral-(or disturbance-) assembly processes were more important than niche processes in low disturbance communities.

These results were very similar to those in a paper by Chase (2007), which we discussed previously in this seminar. Chase (2007) also conducted an experimental study in which the similarity of species composition of communities exposed to varying levels of disturbance was determined. This was a field-based study, though, using species in freshwater ponds where the disturbance was drought. The author also concluded that communities with greater disturbance had more similar species composition than those that weren’t.

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In addition to niche and neutral processes, the results from Jiang and Patel (2008) shed light on the intermediate disturbance hypothesis. This hypothesis states that species diversity is greatest at intermediate levels of disturbance. The intermediate disturbance hypothesis has not been supported in most studies, including in the paper currently being discussed. In Jiang and Patel (2008), only the control treatment had the greatest species richness in the intermediate disturbance regime. This was not the case for any of the other sequences. The authors suggested that the intermediate disturbance hypothesis might only hold for communities which have simultaneous introduction of species, such as in their control, and not sequential introduction, like the other sequences. Because simultaneous introduction rarely occurs in natural systems, it seems unlikely that most systems would exhibit the intermediate disturbance hypothesis.

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In response to the paper by Jiang and Patel (2008), we discussed how to properly frame and focus ecological papers. One criticism of this paper is their attempt to discuss two hypotheses in a single paper, the influence of niche and neutral processes on community assembly and the intermediate disturbance hypothesis. In reference to the former hypothesis, alternative stable states were also mentioned. It is not clear from the title of the paper, and only slightly more clear in the abstract, that the authors are addressing two hypotheses in this paper. We suggest that a better approach may be to choose a single concept and address it more thoroughly than to attempt to pack too much information and too many ideas into one paper.

In Fargione, Brown, and Tilman (2003), experiments on grassland plots were carried out to determine the influence of functional traits on community assembly. At the Cedar Creek LTER, particular numbers of randomly chosen grassland species were planted on 3m x 3m plots of land. After three years, which allowed for these plant species to become established, 27 new species of plants were introduced. The biomass and ground cover increase of these introduced species was determined two years later. All of the plant species were categorized based on traits including resource use into the following four functional groups: legumes, forbs, C3 plants, and C4 plants. The purpose of the experimental study was to determine if it is more unlikely for introduced species of a particular functional guild to become established if there are many resident species of that guild already present due to competitive exclusion. If this does occur, it indicates that nonneutral processes are important in the assembly of these communities.

The first key result was that, regardless of functional groups, greater resident species richness resulted in less introduced species richness. When we examined the figure that presented this data, we questioned the strength of this relationship. The negative relationship between introduced and resident species richness seemed to be driven primarily by the greatest resident species richness value (n = 24). The relationship did not hold for the remaining resident species richness values. The second problem that we identified with this result was that is has no bearing on the research question being asked. The focus of the paper is to use functional traits to determine the relative influences of niche and neutral assembly processes on these communities. Because the functional groups were not distinguished in this result, it tells us nothing about niche or neutral processes. This result only informs us that, when there are more resident species regardless of their traits, there will be fewer species that are able to become established. This is an intuitive conclusion because there are limited resources and, if there are more species present, there are less resources available for newly introduced species.

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The second, more informative result presented in Fargione, Brown, and Tilman (2003) was that the resident species of each functional guild had the “most negative impact” on the introduced species of their own guild. This seems to show that there are niche processes involved in this community’s assembly, because species tended to prevent introduced species with similar traits from being able to become established. This was shown, somewhat unclearly, in a table which I modified for clarity below. Resident species of each guild had the most negative values with the same introduced guild, and these values are in red boxes. If only neutral processes were occurring, each resident functional guild would have the same influence on all of the introduced functional guilds, including its own, and that was not the case.

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While the two papers that we discussed had experiments that used different study systems and organisms, different methodologies, and different questions, they both addressed the relative influence of neutral and niche processes on community assembly. Using protist microcosm experiments, Jiang and Patel (2008) determined that niche processes are more important in high disturbance regimes because disturbance is an environmental filter that prevents non-disturbance resistance species from becoming established. In low disturbance, neutral processes such as dispersal are more important and result in greater variation in community composition. Fargione, Brown, and Tilman (2003) used the influence of functional traits to determine whether niche processes were occurring in the assembly of grassland communities. Because greater abundance of resident species with functional traits prevented functionally similar introduced species from becoming established, it seemed that niche processes were important in their system. 


Signature of dispersal on community structure

This post was contributed by Rodrigo Barbosa Ferreira who is a PhD candidate in Dr. Karen Beard’s lab. Rodrigo is studying the effects of habitat fragmentation on bromeliad-dependent frogs in Brazil, and was recently awarded the CNR graduate researcher of the year. Take it away Rodrigo.

We recently discussed two papers (listed below) on the role of dispersal limitation:

  • Shurin, J. 2000. Dispersal limitation, invasion resistance, and the structure of pond zooplankton communities. Ecology. 81:3074–3086. (pdf)
  • Seidler, T. G., and J. B. Plotkin. 2006. Seed dispersal and spatial pattern in tropical trees. PLoS Biology 4:2132–2137. (pdf)

During our  discussion we attempted to answer some interesting questions such as:
– What is the driving factor structuring a given community in a given area?
– How important is dispersal for structuring communities?
– Is biological diversity an important factor preventing invasion?

The Shurin (2000) paper is an important one to discuss because the author empirically tested two fundamental paradigms in the emerging field of Invasion Ecology. Specifically, Shurin discusses both the role of dispersal and interspecific interactions on structuring the community composition of zooplankton.

Shurin (2000) begins his abstract stating that “for a species to colonize a site it must both arrive there by dispersal from another site and maintain positive population growth in the local environment”. He carried out two experiments which compared the importance of dispersal ability vs. native community resistance in structuring a community. Using zooplankton as study taxon, Shurin set up enclosures in natural ponds and manipulated several additional ponds. He added invasive species to the local communities and evaluated the establishment of invasive populations through time. In this experiment, he found that only a small portion of the introduced species became established (i.e., most introduced species became extinct). In the following year, he conducted a second experiment where he reduced the abundance of native species by filtering the enclosures. He found out an increase in the success of population establishment of the introduced species. He concludes that dispersal plays an important role determining where the species can reach or potentially colonize. However the local community diversity is the decisive factor excluding potential invaders (Shurin 2000, Fig. 2).

shurin_fig2In recent years, a consensus has emerged in the field of Invasion Ecology on the set of important processes related to species invasion. For example, now it is well recognize that propagule pressure has an important contribution to whether or not an  introduced species becomes established. Shurin mentions this in the Material and Methods section and also on the Discussion where he says “some species introduced in low numbers may have failed to invade because too few propagules were introduced”. In my opinion, a key weakness of this study was that it failed to account for propagule pressure despite of acknowledging the importance of it. In addition to the invaders abundance (that he mentioned) as a potential problem on species establishment, the number of introduction events plays also a major role in invasion. For instance, if he had conducted another introduction event in the enclosures perhaps the introduced species would have established via rescue effects.  However, as I said above, propagule pressure was not a totally recognized important factor influencing non-native species establishment at the time of this publication and therefore should not minimize the importance of these brilliant experiments.

The second paper, by Seidler and Plotkin (2006), contributed to our discussion on dispersal by demonstrating the importance of morphological traits on seed dispersal of trees in tropical region. Dispersal limitation is a potential mechanism for separating species in space and reducing competitive exclusion as stated by Seidler and Plotkin (2006). These authors investigated the spatial distribution of trees in a 50-hectare plot of primary tropical forest. By evaluating the dispersal morphologies and fruit sizes of 561 species, these authors clearly show the importance of this species traits on their spatial distribution. Animal-dispersed species exhibited significantly larger cluster sizes than species not dispersed by animals (Seidler and Plotkin, Fig. 2). This study has important theoretical implications, but I found it very interesting that the morphological traits of the plants could be linked to clustering because clustering is well known to reduce alpha diversity at small spatial scales, as well as, increase turnover and thus increase beta and gamma diversity at larger scales.  Thus this paper seems to imply a link between the individuals’ traits and the community diversity properties.


Stochastic and Deterministic Mechanisms of Assembly

Recently in seminar we discussed two influential papers:

  • Vellend, B. M. 2010. Conceptual Synthesis in Community Ecology. The Quarterly Review of Biology 85:183–206. (pdf)
  • Chase, J. M. 2007. Drought mediates the importance of stochastic community assembly. Proceedings of the National Academy of Sciences of the United States of America 104:17430–17434. (pdf)

I chose these papers because I feel that they do a good job of both laying the conceptual and practical groundwork necessary to advance  the debate between the relative importance of stochastic and deterministic processes in community ecology.

Before our discussion began there was a flurry of interesting tweets inspired by the readings:

tweet2 tweetsbeth_ross_tweetThese tweets helped set the tone for our discussion and led to some interesting discussion.

The key questions that we discussed during the seminar were:

Continue reading

Introduction to Community Assembly

The first day of the USU community assembly seminar was a great success. We have a really excellent group of ecologists that seem excited to discuss the latest ideas in community assembly. To get the group all on the same conceptual page and to provide some historical context into the study of community assembly I put together a short lecture that summarizes the existing conceptual framework of community assembly and delves into the origins of the various ideas that it is based upon. The slides to my talk are here, enjoy!

Palmer, M. W. 1994. Variation in species richness – towards a unification of hypotheses. Folia Geobotanica & Phytotaxonomica 29:511–530.

HilleRisLambers, J., P. B. Adler, W. S. Harpole, J. M. Levine, and M. M. Mayfield. 2012. Rethinking Community Assembly through the Lens of Coexistence Theory. Annual Review of Ecology, Evolution, and Systematics 43:227–248.

see the blog’s bibliography for additional references

Seminar Details


Printable Course Flyer (pdf)

Biol 6750 sec 007

Graduate Seminar
1 credit hour

Course Description

This course will explore important contemporary papers (from the last 10 years) that are pioneering new methods of studying ecological community assembly.  The course will be organized as a seminar in which each week a different paper or concept is shared with the group.  The emphasis of the course will be on the intersection of different approaches to understanding community assembly including but not limited to the role of functional traits, phylogenetic conservatism, dispersal limitation, environmental filtering, and eco-evolutionary dynamics.  The papers will cover theoretical, experimental, and data-intensive evidence for the importance of different mechanisms underlying species coexistence, abundance, and spatial and temporal distributions.

Day and Time– Thursday, 2pm in BNR 132

Advanced undergraduates allowed with permission.

If you are interested in attending contact:

Dr. Daniel J. McGlinn
Department of Biology, BNR 132
@danmcglinn on twitter