2.2.1. Species Richness and Phylogenetic Diversity

Fundamental to biodiversity research is the quantification of organismal diversity. Different approaches to this task may provide different interpretations by ecologists, evolutionary biologists, and conservation biologists regarding the role that biodiversity plays in ecosystem function, niche allocation, and species preservation. Phylogenetic diversity was proposed as a metric that quantifies diversity by summing the branch lengths of a given phylogenetic tree [88,89] and is arguably a more descriptive measure of biodiversity than alternative indices such as simple species richness and abundance [90]. DNA barcoding provides an efficient and rapid resource for generating phylogenies to measure phylogenetic diversity, particularly when combined with metabarcoding [91].

It should be noted however that despite the utility of DNA barcoding approaches in diversity assessment, limitations exist. Winter et al. [92] described some of the limitations of phylogenetic diversity insofar as the metric is applied to conservation applications. And although phylogenetic diversity has been lauded as an indicator of species interactions and ecosystem functions [93–95], caution has been urged against using this measure alone to conserve functional trait diversity in ecosystems. The growth of DNA barcode databases and new sequencing methods are facilitating the ability to analyze and understand phylogenetic diversity, but if these data are to be used as predictors for conservation and estimates of ecosystem function, they need to be carefully evaluated in combination with detailed trait databases. Among the earliest uses of DNA barcoding to quantify biodiversity were investigations of community assembly and function in long-term forest monitoring plots in Panama.

### 2.2.2. BCI as an Exemplar Tropical Field Site for DNA Barcoding

More than a decade ago the first community phylogeny based on DNA barcode sequence data was published for the trees in a forest dynamics plot on Barro Colorado Island (BCI) in Panama [62]. This publication set off a storm of new investigations that were able to add a well-supported evolutionary perspective to understanding species diversity and assembly in plant communities (e.g., [96–100]). The DNA barcode phylogeny generated for the approximately 300 species of trees on BCI also served as a template for a number of investigations of functional traits. The evolutionary context of such characteristics as soil associations [101], leaf toughness [102], wood nitrogen concentration and life-history strategies [103], foliar spectral traits [104], and anti-herbivore defense traits [105] was found to vary in each of these functional traits across the tree species in the BCI plot. Although some have concluded that phylogenetic indictors are not always tied to ecological determinants of community assembly [106], both phylogenetic- and trait-based approaches have greatly enhanced the understanding of community structure and function on BCI.

Belowground interactions among species have also been investigated at BCI using the DNA barcode library for trees. Jones et al. [107] mapped the belowground distribution of all trees and lianas greater than one centimeter in diameter using their genetic DNA barcode signature. Comparing underground species distributions with aboveground distributions showed that species interactions and spatial overlap was greater belowground than expected based on aboveground stem densities. Although this study raised several questions about methodology and analysis, it concluded that the potential for using DNA barcodes in this type of investigation was high.

The DNA barcode library for trees on BCI has now been expanded to include many of the shrubs and lianas as well as some epiphytes that occur in the forest on the island. Efforts to build DNA barcode libraries and apply DNA barcode methodologies to other groups of organisms (e.g., insects [108]) are underway. This rich genetic resource will greatly enhance future studies of ecological interactions and evolutionary signal in this tropical forest community in Panama.
