Abstract
To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family‐level phylogeny. Here, we use general linear mixed‐effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family‐level phylogeny to estimate topology‐based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family‐level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family‐level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top‐rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family‐level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.
Highlights
Plant DNA barcodes, based on either single or multilocus regions of the chloroplast and/or nuclear genomes, have been applied to questions in community ecology (Kress et al, 2009; Valentini, Pompanon, & Taberlet, 2009)
Our results reveal that multilocus barcodes outperform single‐ locus barcodes in explaining maximum variation in estimates of phylogenetic diversity regardless of the phylogenetic reconstruction methods used, both in terms of model ranking and model‐averaged, standardized effects
The reason for the complementary influence of DNA barcodes with different rates of evolution might be due to different ecological and evolutionary processes operating at different evolutionary time scales, which contribute differently to plant community phylogenetic structure (Mazel et al, 2016)
Summary
Plant DNA barcodes, based on either single or multilocus regions of the chloroplast and/or nuclear genomes, have been applied to questions in community ecology (Kress et al, 2009; Valentini, Pompanon, & Taberlet, 2009). In contrast to the branch length‐based metrics, several phylogenetic diversity metrics (e.g., PAE, the relationship between species evolutionary distinctiveness and abundance; IAC, the imbalance of abundances at higher clades) have been developed to capture information on both the topology and branch lengths of phylogenies connecting the species of a community (Cadotte et al, 2010; Krajewski, 1994; Vanewright, Humphries, & Williams, 1991). These topology‐based metrics have been shown to be valuable for.
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