The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.T he most difficult challenge for DNA barcoding in plants is discriminating among taxa of highly speciose genera where rates of species identification by using a variety of putative barcodes rarely exceed 70% (1). In some cases of complex recently evolved species groups DNA barcoding may simply be inappropriate as an identification tool (2). This difficulty is especially acute in cases where certain life history traits have affected the rates of molecular evolution in a lineage, which in turn may affect rates of species assignment by DNA barcodes [e.g., generation times (3) and age-of-crown group diversification (4)].In the absence of a universal barcode region capable of discriminating among all species in all groups of plants, it is clear that DNA barcodes will be most effectively applied in the identification of a circumscribed set of species that occur together in a floristic region or ecological community, rather than in distinguishing among an exhaustive sample of taxonomically closely related species. In these cases only a limited number of closely related species occur in the same region, so identification to genus is all that is required.It is now generally agreed that a plant barcode will combine more than one locus (5-7) and will include a phylogenetically conservative coding locus (rbcL) with one or more rapidly evolving regions (part of the matK gene and the intergenic spacer trnH-psbA). Although more laborious than a si...

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.

The above-ground biomass (AGB) of tropical forests is a crucial variable for ecologists, biogeochemists, foresters and policymakers. Tree inventories are an efficient way of assessing forest carbon stocks and emissions to the atmosphere during deforestation. To make correct inferences about long-term changes in biomass stocks, it is essential to know the uncertainty associated with AGB estimates, yet this uncertainty is rarely evaluated carefully. Here, we quantify four types of uncertainty that could lead to statistical error in AGB estimates: (i) error due to tree measurement; (ii) error due to the choice of an allometric model relating AGB to other tree dimensions; (iii) sampling uncertainty, related to the size of the study plot; (iv) representativeness of a network of small plots across a vast forest landscape. In previous studies, these sources of error were reported but rarely integrated into a consistent framework. We estimate all four terms in a 50 hectare (ha, where 1 ha = 10(4) m2) plot on Barro Colorado Island, Panama, and in a network of 1 ha plots scattered across central Panama. We find that the most important source of error is currently related to the choice of the allometric model. More work should be devoted to improving the predictive power of allometric models for biomass.

The above-ground biomass (AGB) of tropical forests is a crucial variable for ecologists, biogeochemists, foresters and policymakers. Tree inventories are an efficient way of assessing forest carbon stocks and emissions to the atmosphere during deforestation. To make correct inferences about long-term changes in biomass stocks, it is essential to know the uncertainty associated with AGB estimates, yet this uncertainty is rarely evaluated carefully. Here, we quantify four types of uncertainty that could lead to statistical error in AGB estimates: (i) error due to tree measurement; (ii) error due to the choice of an allometric model relating AGB to other tree dimensions; (iii) sampling uncertainty, related to the size of the study plot; (iv) representativeness of a network of small plots across a vast forest landscape. In previous studies, these sources of error were reported but rarely integrated into a consistent framework. We estimate all four terms in a 50 hectare (ha, where 1 ha = 10 4 m 2) plot on Barro Colorado Island, Panama, and in a network of 1 ha plots scattered across central Panama. We find that the most important source of error is currently related to the choice of the allometric model. More work should be devoted to improving the predictive power of allometric models for biomass.

Abstract:Tropical forest demography and dynamics were examined in three inventory plots across a precipitation gradient in central Panama. The harsh dry season of 1998 that accompanied the 1997-98 El Niño was spanned by censuses at all three sites. The wet and intermediate plots were similar in total species richness, the dry site somewhat lower in diversity; all three sites differed substantially from each other in species composition. Forest-wide growth of large trees was higher at the wet and intermediate sites than at the dry site, but sapling growth was highest at the dry site and lowest at the intermediate site. Forest-wide growth differences were reflected by individual species, for example, saplings of species at the dry site grew faster than saplings of the same species at the intermediate site. Forest-wide mortality was lowest at the dry site and highest at the wet, and this difference was also reflected by individual species. We suggest that low mortality and growth in the drier forest was due to the longer annual dry season and higher deciduousness, and that high sapling growth at the dry site was due to greater light penetration to the forest floor. Growth rates were elevated at aU three sites during 1998, possibly due to reduced cloud-cover during the El Niño. Contrary to expectation, mortality during 1998 was not elevated at wet and intermediate sites during the El Niño drought, but was at the dry site. Finally, we found that some species performed poorly at one site and declined in abundance, while having stable or increasing populations at another site, demonstrating that the communities are not at equilibrium.