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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.

SUBMITTER: Kress WJ

PROVIDER: S-EPMC2763884 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Project description:DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses.

Project description:Tropical forests are globally important for biodiversity conservation and climate change mitigation but are being converted to other land uses. Conversion of seasonally dry tropical forests (SDTF) is particularly high while their protection is low. Secondary succession allows forests to recover their structure, diversity and composition after conversion and subsequent abandonment and is influenced by demographic rates of the constituent species. However, how these rates vary between seasons for different plant sizes at different successional stages in SDTF is not known. The effect of seasonal drought may be more severe early in succession, when temperature and radiation are high, while competition and density-dependent processes may be more important at later stages, when vegetation is tall and dense. Besides, the effects of seasonality and successional stage may vary with plant size. Large plants can better compete with small plants for limiting resources and may also have a greater capacity to withstand stress. We asked how size-dependent density, species density, recruitment and mortality varied between seasons and successional stages in a SDTF. We monitored a chronosequence in Yucatan, Mexico, over six years in three 0.1 ha plots in each of three successional stages: early (3-5 years-old), intermediate (18-20 years-old) and advanced (>50 years-old). Recruitment, mortality and species gain and loss rates were calculated from wet and dry season censuses separately for large (diameter > 5 cm) and small (1-5 cm in diameter) plants. We used linear mixed-effects models to assess the effects of successional stage, seasonality and their changes through time on demographic rates and on plant and species density. Seasonality affected demographic rates and density of large plants, which exhibited high wet-season recruitment and species gain rates at the early stage and high wet-season mortality at the intermediate stage, resulting in an increase in plant and species density early in succession followed by a subsequent stabilization. Small plant density decreased steadily after only 5 years of land abandonment, whereas species density increased with successional stage. A decline in species dominance may be responsible for these contrasting patterns. Seasonality, successional stage and their changes through time had a stronger influence on large plants, likely because of large among-plot variation of small plants. Notwithstanding the short duration of our study, our results suggest that climate-change driven decreases in rainy season precipitation may have an influence on successional dynamics in our study forest as strong as, or even stronger than, prolonged or severe droughts during the dry season.

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

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