Dataset Information

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China.

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.

SUBMITTER: Liu J

PROVIDER: S-EPMC6509380 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China.

Liu Jiajia J Liu Juan J Shan You-Xia YX Ge Xue-Jun XJ Burgess Kevin S KS

Ecology and evolution 20190403 9

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 backbon ...[more]

PMID: 31110686

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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:Species recovery after forest disturbance is a highly studied topic in the tropics, but considerable debate remains on the role of secondary forests as biodiversity repositories, especially regarding the functional and phylogenetic dimensions of biodiversity. Also, studies generally overlook how alpha and beta diversities interact to produce gamma diversity along successional gradients.We used a metacommunity approach to assess how species sorting (i.e., environmental filtering) and mass effect (i.e., source-sink dynamics) affect 14 complementary metrics of amphibian taxonomic, functional, and phylogenetic diversity along a successional gradient in southern Mexico. As amphibians have narrow environmental tolerances and low dispersal capabilities, we expected that species sorting may be relatively more important than mass effect in structuring amphibian communities.Between 2010 and 2012, we sampled frogs, salamanders, and caecilians in 23 communities distributed in four successional stages: young (2-5 years old) and intermediate (13-28 years old) secondary forests, old-growth forest fragments, and old-growth continuous forest. We assessed 15 ecologically relevant functional traits per species and used a time-calibrated molecular phylogeny.We recorded 1,672 individuals belonging to 30 species and 11 families. Supporting our expectations from the species sorting perspective, from the poorest (younger forests) to the best quality (continuous forest) scenarios, we observed (a) an increase in alpha diversity regardless of species abundances; (b) a clear taxonomic segregation across successional stages; (c) an increase in functional richness and dispersion; (d) an increase in mean phylogenetic distance and nearest taxon index; and (e) a reduction in mean nearest taxon distance. However, 10 species occurred in all successional stages, resulting in relatively low beta diversity. This supports a mass effect, where interpatch migrations contribute to prevent local extinctions and increase compositional similarity at the regional scale.Our findings indicate that amphibian metacommunities along forest successional gradients are mainly structured by species sorting, but mass effects may also play a role if high levels of forest cover are conserved in the region. In fact, secondary forests and forest fragments can potentially safeguard different aspects of amphibian diversity, but their long-term conservation value requires preventing additional deforestation.

Dataset Information

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China.

Publications

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China.

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