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

Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China

DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.

Species pool size and rainfall account for the relationship between biodiversity and biomass production in natural forests of China

The strength of biodiversity-biomass production relationships increases with increasing environmental stress and time. However, we know little about the effects of abiotic (e.g., climate) and biotic (e.g., species pool and community composition) factors on this trend. Whether variation in biomass production is best explained by phylogenetic diversity metrics or traditional measures of species richness also remains elusive. We compiled estimates of community composition and biomass production for tree species in 111 permanent quadrats spanning three natural forests (tropical, subtropical, and temperate) in China. Based on ~10 years of data, we compared temperature, rainfall, species pool size, and community composition in each forest each year. We estimated species richness and phylogenetic diversity in each quadrat each year; the latter metric was based on the sum of branch lengths of a phylogeny that connects species in each quadrat each year. Using generalized linear mixed-effect models, we found that top-ranked models included the interaction between forest and biodiversity and the interaction between forest and year for both biodiversity metrics. Variation in biomass production was best explained by phylogenetic diversity; biomass production generally increased with phylogenetic diversity, and the relationship was stronger in subtropical and temperate forests. Increasing species pool size, temperature, and rainfall and decreasing inter-quadrat dissimilarity range shifted the relationship between biomass production and phylogenetic diversity from positive to neutral. When considered alone, species pool size had the strongest influence on biomass production, while species pool size, rainfall, and their interaction with phylogenetic diversity constituted the top-ranked model. Our study highlights the importance of species pool size and rainfall on the relationship between phylogenetic diversity and biomass production in natural forest ecosystems.

Lack of Phylogenetic Differences in Ectomycorrhizal Fungi among Distinct Mediterranean Pine Forest Habitats

Understanding whether the occurrences of ectomycorrhizal species in a given tree host are phylogenetically determined can help in assessing different conservational needs for each fungal species. In this study, we characterized ectomycorrhizal phylogenetic composition and phylogenetic structure in 42 plots with five different Mediterranean pine forests: i.e., pure forests dominated by P. nigra, P. halepensis, and P. sylvestris, and mixed forests of P. nigra-P. halepensis and P. nigra-P. sylvestris, and tested whether the phylogenetic structure of ectomycorrhizal communities differs among these. We found that ectomycorrhizal communities were not different among pine tree hosts neither in phylogenetic composition nor in structure and phylogenetic diversity. Moreover, we detected a weak abiotic filtering effect (4%), with pH being the only significant variable influencing the phylogenetic ectomycorrhizal community, while the phylogenetic structure was slightly influenced by the shared effect of stand structure, soil, and geographic distance. However, the phylogenetic community similarity increased at lower pH values, supporting that fewer, closely related species were found at lower pH values. Also, no phylogenetic signal was detected among exploration types, although short and contact were the most abundant types in these forest ecosystems. Our results demonstrate that pH but not tree host, acts as a strong abiotic filter on ectomycorrhizal phylogenetic communities in Mediterranean pine forests at a local scale. Finally, our study shed light on dominant ectomycorrhizal foraging strategies in drought-prone ecosystems such as Mediterranean forests.

Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies

Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics.

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

Diversification of African Tree Legumes in Miombo-Mopane Woodlands

The southern African Miombo and Mopane ecoregions constitute a unique repository of plant diversity whose diversification and evolutionary history is still understudied. In this work, we assessed the diversity, distribution, and conservation status of Miombo and Mopane tree legumes within the Zambezian phytoregion. Data were retrieved from several plant and gene databases and phylogenetic analyses were performed based on genetic barcodes. Seventy-eight species (74 from Miombo and 23 from Mopane, 19 common to both ecoregions) have been scored. Species diversity was high within both ecoregions, but information about the actual conservation status is scarce and available only for ca. 15% of the species. Results of phylogenetic analyses were consistent with current legume classification but did not allow us to draw any conclusion regarding the evolutionary history of Miombo and Mopane tree legumes. Future studies are proposed to dissect the diversity and structure of key species in order to consolidate the network of conservation areas.