Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes.

BACKGROUND AND AIMS: Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. METHODS: A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. KEY RESULTS: Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). CONCLUSIONS: Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

[Physiochemical properties and microbial community characteristics of rhizosphere soil in Parashorea chinensis plantation]. / æœ›å¤©æ ‘äººå·¥æž—æ ¹é™ åœŸå£¤ç†åŒ–æ€§è´¨åŠå¾®ç”Ÿç‰©ç¾¤è½ç‰¹å¾.

We explored the impacts of different mixed trees on the improvement of soil microecological environment in rhizosphere of Parashorea chinensis, including pure P. chinensis plantation (WC), mixed P. chinensis and Dalbergia odorifera plantation (WJ), mixed P. chinensis and Eucalyptus urophylla × E. grandis plantation (WA). Soil physical and chemical properties were analyzed. The characteristics and distribution of soil microbes in the rhizosphere were measured by the methods of Biolog-Eco micro plate and phospholipid fatty acid methyl ester (PLFA). Soil water content, soil pH, organic matter, total nitrogen, total potassium content and the activities of sucrase, urease and acid phosphatase in rhizosphere soil of WA were significantly higher than those of WC and WJ, without difference between WC and WJ. There were no significant differences in the contents of nitrate nitrogen, ammonium nitrogen, and available potassium between WA and WJ, which were obviously higher than those in WC. There were significant differences in total phosphorus and available phosphorus contents among the three stands, with an order of WJ>WA>WC. The average color change rate (AWCD), Shannon index, Simpson index, McIntosh index and the utilization of six types of carbon source substrates in microorganisms were the highest in the rhizosphere soil of WA, followed by WJ and WC. Results of principal component analysis showed that carbohydrates, amino acids and phenolic acids were the main carbon sources for microbial utilization. In WA, the PLFA content of rhizosphere soil microorganism, bacteria, fungi and actinomycetes was the highest, followed by WJ and WC. There were significant positive correlation between soil physical and che-mical properties and the microbial characteristics. Combining the physical and chemical properties of soil and the functional and structural characteristics of microbial communities, the mixed P. chinensis and E. urophylla × E.grandis plantation may be most conductive to the improvement of the rhizosphere microecological environment and increase soil available nutrients at the young tree phase of P. chinensis.

Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method.

BACKGROUND: Competitive interactions in biological communities can be thought of as giving rise to "assembly rules" that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an "ant mosaic", in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess presence of ant mosaics in a hitherto under-investigated forest stratum, the emergent trees of the high canopy in primary tropical rain forest, and explore how the strength of any ant mosaics is affected by spatial scale, time of day, and sampling method. METHODS: To test whether these factors might impact the detection of ant mosaics in pristine habitats, we sampled ant communities from emergent trees, which rise above the highest canopy layers in lowland dipterocarp rain forests in North Borneo (38.8-60.2 m), using both baiting and insecticide fogging. Critically, we restricted sampling to only the canopy of each focal tree. For baiting, we carried out sampling during both the day and the night. We used null models of species co-occurrence to assess patterns of segregation at within-tree and between-tree scales. RESULTS: The numerically dominant ant species on the emergent trees sampled formed a diverse community, with differences in the identity of dominant species between times of day and sampling methods. Between trees, we found patterns of ant species segregation consistent with the existence of ant mosaics using both methods. Within trees, fogged ants were segregated, while baited ants were segregated only at night. DISCUSSION: We conclude that ant mosaics are present within the emergent trees of the high canopy of tropical rain forest in Malaysian Borneo, and that sampling technique, spatial scale, and time of day interact to determine observed patterns of segregation. Restricting sampling to only emergent trees reveals segregatory patterns not observed in ground-based studies, confirming previous observations of stronger segregation with increasing height in the canopy.