Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo

Abstract

Community phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES-MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES-MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES-MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.

Keywords: DNA barcoding; South‐East Asia; community phylogeny; tropical rainforest.

FIGURE 1

A view of the forest canopy in Lambir Hills national park. Photo taken from a canopy tower in the park.

FIGURE 2

Location of Lambir Hills National Park. The map was created using R package “maps” (Becker & Wilks, 1993, 1995).

FIGURE 3

Setting in simulation analysis. (a and b) spatial structures of environmental types of two virtual plots. Color of each cell indicates environmental types. (a) the spatial structure is divided into two major areas with environmental types. (b) the spatial structure with disparate environmental types. (c) Phylogenetic structures of species' habitat niche. Color of each square indicates species' habitat niche corresponding to environmental type of the same color. There are 9 patterns of species' niche with various strength of phylogenetic signal.

FIGURE 4

Images of simulations. (a) the process of creating a virtual community with the first row of the species’ habitat niche (number one in Figure 2c), and a structured habitat (Figure 2a). For each cell in the virtual plot, four species were randomly selected with a niche corresponding to the environment of the cell. (b) Separation images with different plot sizes in the virtual community. The plot was prepared in four different sizes: 1 × 1, 2 × 2, 4 × 4, and 8 × 8 cells.

FIGURE 5

Correlation of phylogenetic diversity indices calculated with Phylomatic tree and DNA barcode tree for four plot sizes. The break line is a straight line with slope 1 passing through the origin.

FIGURE 6

Relationships between the difference in phylogenetic diversity between plots and the probability of matching the rank of phylogenetic diversity values. Lines are logistic regression lines. The horizontal axis is the difference in phylogenetic diversity between the two plots. The vertical axis is the probability that plots with high‐phylogenetic diversity values match between the Phylomatic tree and the DNA barcode tree. Solid lines indicate SES–MPD, and dashed lines indicate SES–MNTD. Colors indicate plot size: Green 10 × 10 m², orange 20 × 20 m², purple 50 × 50 m², and red 100 × 100 m², respectively.

FIGURE 7

Phylogenetic diversity indices were calculated by Phylomatic (a and b) tree and DNA barcode (c and d) tree for four plot sizes.

FIGURE 8

Changes in mean values of phylogenetic diversity indices with changes in plot size in simulations. The upper panel shows the results with the plot environment divided into two large plots as Figure 1a. The lower panel shows the results with the plot environment randomly arranged as Figure 1b. The colors of the lines indicate the respective sets of habitat niches in Figure 1c. In both MNTD plots, the line for set 1 overlap completely below the line for set 2.