Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

Abstract

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...

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

“…In neighborhood analyses, the relationship between focal plant performance and phylogenetic relatedness to neighbors was insignificant, significantly positive and significantly negative in 105, 19 and 21 tests, respectively (Lebrija-Trejos et al 2014). For studies of phylogenetic dispersion, the full range of phylogenetic community structure has been detected, with phylogenetic composition more similar, more dissimilar or indistinguishable from chance expectation in different 20-by-20-m quadrats at two of our sites (Kress et al 2009, Pei et al 2011. A modification of this approach compares a metric of phylogenetic community composition among life stages.…”

“…At each site there is a large, fully enumerated Forest Dynamics Plot (FDP) in which all free-standing woody stems ≥1 cm DBH have been measured, mapped to the nearest 0.5 m and identified to species using standardized protocols (Condit 1998, Anderson-Teixeira et al 2015. Molecular phylogenies were constructed for woody species in these FDPs using three barcode loci (rbcL, matK and trnH-psbA) (Kress et al 2009, Kress et al 2010, Pei et al 2011. In this study, we used a single dated mega-phylogeny that was constructed simultaneously based on the DNA barcode sequence data in different ForestGEO plots (Erickson et al 2014).…”

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…Different approaches exist for matching an unknown query sequence with sequences in a reference database or library and tend to be based on ad hoc criteria which may include the frequency of the highest hits, percentage sequence similarity, bootstrapping, BLAST scores or tree‐based clustering assessment (Kress et al., 2009; Wilson et al. 2011).…”

“…In this study, NJ trees were used to establish clustering of query sequences into correct genus‐specific groups with strong bootstrap support and were not used to infer phylogeny. Poor resolution in tree topologies with low bootstrap scores and polytomies obtained for rbcL sequences were obtained which may be due to inadequate low genetic distances for most species (Hebert et al., 2003; Hollingsworth et al., 2016; Kress et al., 2009; Ross et al., 2008; Wilson et al. 2011).…”

DNA barcoding in floral and faunal research

“…The large-scale inventory of caterpillars, their hosts and their parasites in Costa Rica has provided an excellent example of how barcoding has changed the basic approach to an inventory project, starting with sampling, processing, identification, analysis, and even changing the approach to publication of results (Janzen et al, 2009; Hallwachs 2011a, 2011b; see also Strutzenberger et al, 2010). In addition to the changes in work flow there have been significant impacts, from finding cryptic species to matching dimorphic males and females, which have substantially improved the quality and depth of the inventory, but also greatly multiplied the number of situations requiring further taxonomic work for resolu- (Kress et al, 2009(Kress et al, , 2010Costion et al, 2011). Perhaps even greater opportunities for improving the speed and quality of inventories exist in the marine realm, where poorly known larval stages exist in vast quantities, and species concepts must be compared across vast oceanic distances (Goetze, 2010;Heimeier et al, 2010;Hubert et al, 2010;Stern et al, 2010;Plaisance et al, 2011;Ranasinghe et al, 2012).…”