using phylogenetics in understanding community dynamics

This essay stems from the Webb paper on exploring the phylogenetic structure of a tree community in Borneo (2000). I chose the study because I was particularly interested in the idea of using phylogenetic approach in understanding ecological communities; that you can somehow trace ecological processes operating in a community (general; community perspective) by looking at the degree of relatedness of species within that community (specific; clade perspective). This novel approach is nothing less than brilliant, as it has even given birth to a new area of study. However, it does have some yet unresolved issues, some of which I discuss here.

Researchers have taken various approaches to this consolidation of phylogenetics and community ecology. Phylogenetics is used in the study of community assemblages and community niche structure. Looking at it from the flip side, a community context can be included to studies of trait evolution (Webb et al, 2002). The justification for such studies is the possibility that there is a direct link between the evolutionary relatedness of organisms in a community with the ecological processes that determine their distribution (Kraft, 2007).

As more and more studies are being conducted along these lines, Losos (2008) stressed the importance of not anchoring them on the assumption that closely related species are ecologically similar. Phylogenetic signals may or may not be detected, depending on the clades and the traits. And for some studies, signals are detected, but are negatively correlated with ecological similarity. A study on sunfish communities showed that opposite phylogenetic patterns (clustering and overdispersal) that simultaneously operate also tend to cancel each other out overall (Helmus et al, 2007). The differing results from the studies he reviewed led him to conclude that phylogenetic signals do occur, but are not ubiquitous. Another thing to consider is that ecological characters have low phylogenetic signal, lower than morphological and physiological traits.

Webb’s study on Bornean trees gave a clear indication that the community was not randomly structured, and that related species tend to co-occur. But work on the community of neotropical trees in Panama (Kembel&Hubbell, 2006) resulted in a close to random phylogenetic structure at all spatial scales. However, a closer examination of phylogenetic structure across different habitats did produce patterns of clustering and overdispersal. The varying patterns seen in this study thus highlight the importance of defining the community that you are studying, as the definition for a community is usually arbitrary. According to Webb et al (2002), phylogenetic and phenotypic attraction and repulsion are largely dependent on scale. Also, at the continental scale, biogeographic, not ecological, processes influence phylogenetic patterns.

Another important matter to consider is the conservativism of the traits that are being examined. The Webb review paper (2002) contains a table on the expected distribution of taxa on the phylogeny, given the community assembly process (habitat filtering or exclusion) and trait evolution (conserved or convergent). It showed that phylogenetic clustering or overdispersal is dependent not only on the type of assembly but also on trait evolution. For the phylogenetic clustering that Webb (2000) observed in Bornean trees, he assumed that ecological traits are conserved, and hence was able to conclude that habitat filtering structured that particular community. The situation is more complicated if the co-occurring species are distantly related. If the traits are conserved, their coexistence may be explained by competitive exclusion among the conspecifics/congeners. If they are convergent, habitat filtering can account for it (Kraft, 2007). Hence, generalizations on the processes that operated on the community (habitat partitioning, negative density dependence, etc) cannot readily be drawn from the generated phylogenetic structure without knowledge of the evolution of the traits. This is supported by a study conducted by Kraft et al (2007) where simulations with strongly conserved traits produced strong signals of phylogenetic community structure, and weaker signals for less conserved ones.

The construction of the phylogenetic tree also presents some limitations. Webb (2002) enumerated some of these, and presented a very simplistic solution that can pose some problems when used for species pairs, but can be corrected by increasing the sample size. It is along this line of creative thinking that I derive my confidence in this relatively new field of study. Researchers are aware of the limitations that the current methodologies present, and they are constantly looking at ways of futher reducing them.

However numerous, valid, and important all these unresolved matters concerning phylogenetic ecology are, the good things outweigh the bad. As always. The field of phylogenetics, by itself, is complex, and its application to something as complicated as community dynamics makes it doubly difficult. A phylogenetic tree is in itself a hypothesis, and its use in studies on ecological communities is predicated on assumptions that may be justified, but they are assumptions nonetheless. However, a significant contribution that these studies have brought is the added dimension of phylogenetic relatedness of species in examining community diversity and species coexistence (Webb et al, 2002). There are even more advantages this field presents, and clearly, it doesn’t stop here. As more studies will be conducted in this field, the lesser the assumptions will be, the more definite the concepts become, and the better we understand the dynamics of ecological communities.

Assigned Reading:
Webb, C. O. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. 2000. The American Naturalist 156:145-155.

References:
Helmus, M. R., K. Savage, M. W. Diebel, J. T. Maxted and A. R. Ives. 2007. Separating the determinants of phylogenetic community structure. Ecological Letters 10:917-925.

Kraft, N. J. B., W. K. Cornwell, C. O. Webb, and D. D. Ackerley. 2007. Trait evolution, community assembly, and the phylogenetic structure of ecological communities. The American Naturalist 170:271-283.

Kembel, S. W. and S. P. Hubbell. 2006. The phylogenetic structure of a neotropical forest tree community. Ecology, 87(7) Supplement:S86-S99.

Losos, J. B. 2008. Phylogenetic niche conservativism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11:995-1007.

Webb, C. O., D. D. Ackerley, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475-505.