Phylogenetic trees have been extensively used in community ecology.
However, how the phylogenetic reconstruction affects ecological
inferences is poorly understood. In this study, we reconstructed three
different types of phylogenetic trees (a synthetic-tree generated using
VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a
genome-tree generated from plastid genomes) that represented an
increasing level of phylogenetic resolution among 580 woody plant
species from six dynamic plots in subtropical evergreen broadleaved
forests of China. We then evaluated the performance of each phylogeny in
estimations of community phylogenetic structure, turnover and
phylogenetic signal in functional traits. As expected, the genome-tree
was most resolved and most supported for relationships among species.
For local phylogenetic structure, the three trees showed consistent
results with Faith’s PD and MPD; however, only the synthetic-tree
produced significant clustering patterns using MNTD for some plots. For
phylogenetic turnover, contrasting results between the molecular trees
and the synthetic-tree occurred only with nearest neighbor distance. The
barcode-tree agreed more with the genome-tree than the synthetic-tree
for both phylogenetic structure and turnover. For functional traits,
both the barcode-tree and genome-tree detected phylogenetic signal in
maximum height, but only the genome-tree detected signal in leaf width.
This is the first study that uses plastid genomes in large-scale
community phylogenetics. Our results highlight the outperformance of
genome-trees over barcode-trees and synthetic-trees for the analyses
studied here. Our results also point to the possibility of Type I and II
errors in estimation of phylogenetic structure and turnover and
detection of phylogenetic signal when using synthetic-trees.