Methods for community ecology
Why so many desert plant communities are dominated by spiny species, most of them cacti? The first observation refers to the community’s phenotypic structure and the second to its phylogenetic structure. What do these observations tell us about the mechanisms assembling these communities?
The way communities are assembled is an old ecological question currently experiencing renewed interest thanks to the recent advances in molecular biology and phylogenetics. The generality of these new methods has allowed us to understand the structure of communities of organisms from different kingdoms and at different scales. Concomitant with this growing interest, new methods, metrics, terms, and software have appeared that independently solve similar questions, but with different approaches. In this new paper we provide a unifying framework on methods for community structure based on the relationships between four key concepts: phylogeny, phenotype, environment, and co-occurrence. The different approaches are based on different community representations of traits, the phylogenetic relationships of species in the community, or species occurrence along the environmental gradients. We finally provide insights on future directions of this emerging discipline.
Figure 1. Methods for analyzing community structure can be represented in a simple framework in which the relationships (arrows) between the four key concepts (phylogeny, phenotype, environment, and co-occurrence) are integrated. The numbers in brackets refer to:
(1) Co-occurrence pattern versus the random expectation
(2) Phenotype-based approach:
(2.1) Relationship between the species' phenotypes and their co-occurrence (phenotypic community structure).
(2.2) Relationship between species response to the environment and the species phenotypes, controlling by the species' phylogenetic relatedness (phenotypic community structure).
(3) Phylogeny-based approach:
(3.1) Relationship between the species' phylogenetic relationships and their co-occurrence (phylogenetic community structure).
(3.2) Relationship between the species' phenotypes and their phylogenetic relationships (trait evolution).
(4) Environment-based approach: relationship between species response to the environment and the co-occurrence, considering the phylogenetic relatedness (phylogenetic community structure).
See previous post [link] on the effect of fire in phenotypic and phylogenetic structure of communities.