Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Abstract

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.

DNA barcodes for ecology, evolution, and conservation

“…As more DNA barcode data are assembled, an increased number of taxa will be woven into increasingly larger phylogenies. This approach results in more well-supported phylogenetic reconstructions of the constituent species from which individual community phylogenies may be pruned out for targeted analysis [35]. Furthermore, the use of a constraint tree derived from existing Tree of Life studies will enforce topological relations at deeper phylogenetic levels, where the limited signal from the small amount of nucleotide data provided by the DNA barcode markers is most problematic (Figure 3) [27].…”

“…The improvement of topological resolution through incorporation of DNA barcode data for all or most species in the community improves the power of evolutionary-based hypothesis testing in an ecological framework. Since that first DNA barcode-based community phylogeny, similar investigations have focused on other forests in the tropics [27,35]. A major challenge of reconstructing a phylogenetic tree using DNA barcode sequence data is to capture the proper evolutionary relations among both highly divergent as well as closely related species.…”

“…Advancing our understanding of the processes that structure beta diversity will require data on species performance and community composition collected across environmental gradients (e.g., soil or precipitation) and at multiple spatial and temporal scales. The relative ease of generating universal DNA barcode data for plants in a community will facilitate these broad spatial comparisons and is currently being carried out across forest dynamics plots around the globe [35].…”

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

“…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). Most species without…”

Draba bruce-bennettii(Brassicaceae), a Remarkable New Species from Yukon Territory, Canada

“…A unique challenge for plants is that plastid and nuclear DNA barcodes yield lower species resolution compared to the mitochondrial and nuclear barcodes used for animals and fungi (Naciri and Linder, 2015;Hollingsworth et al, 2016). However, building a geographically circumscribed reference library can improve the effectiveness of plant DNA barcoding (Clerc-Blain et al, 2010;Burgess et al, 2011;de Vere et al, 2012;Parmentier et al, 2013;Elliott and Davies, 2014;Erickson et al, 2014). Braukmann et al (2017a) recently showed that the discriminatory power of the most commonly used plant DNA barcodes (rbcL, matK, and ITS2) for the Canadian vascular plant species varies depending on the method of analysis (BLAST vs. Mothur) and biogeographic region (e.g., Canadian arctic vs. woodland).…”