Abstract
BackgroundSpecies number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.Methodology/Principal FindingsHere we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.Conclusions/SignificanceAs first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.
Highlights
Understanding how species are assembled into natural communities in both primary and secondary forests is a major endeavor of investigation by community ecologists, especially in species-rich tropical biomes [1,2,3]
This procedure has proven useful in building community phylogenies, they are in many cases incompletely resolved, and by extension, may have less statistical power than more fully resolved phylogenies to ascertain relationships between functional traits, community ecology, and evolutionary history [11]
They found on Barro Colorado Island (BCI) that the average phylogenetic structure was close to random and concluded that in some cases evolutionarily conserved traits were favored in stressful habitats, whereas species composition in the slope and swamp habitats may have been driven by ecological interactions, such as competition
Summary
Understanding how species are assembled into natural communities in both primary and secondary forests is a major endeavor of investigation by community ecologists, especially in species-rich tropical biomes [1,2,3]. This procedure has proven useful in building community phylogenies (see below), they are in many cases incompletely resolved (particular in poorly studied taxa), and by extension, may have less statistical power than more fully resolved phylogenies to ascertain relationships between functional traits, community ecology, and evolutionary history [11] Forest dynamics plots, such as the 50-ha plot on Barro Colorado Island (BCI) in Panama, in which all of the woody plant species have been identified, mapped, and periodically censussed [12,13] have provided the opportunity to test various conceptual ideas on the rules that govern community assembly, such as the Neutral Theory of Biodiversity [14]. In that study sequence data from three barcode loci were used to generate a well-resolved specieslevel phylogeny
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
