Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae).

Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.

Selection pressure causes differentiation of the SPL gene family in the Juglandaceae.

The SQUAMOSA promoter-binding protein-like (SPL) is a plant-specific transcription factor that influences flowering and vegetative development. Although the SPL genes have been functionally analyzed in many species, studies on the evolutionary history of the whole gene family, and in the Juglandaceae specifically, have been limited. Here, we conducted a phylogenetic relationship analysis of the Juglandaceae SPL gene family compared with other land plant species. Our results showed that the SPL genes were divided into three major clades, all of which were further divided into ten small clades. Selection pressure analysis suggested that all SPL genes were exposed to purifying selection pressure during evolution. The purifying selection was smaller for the Juglandaceae SPL genes than for other angiosperms, indicating a greater susceptibility to functional differentiation in the Juglandaceae. The SPL proteins encoded by Clade 1 contained a branch-specific transmembrane structure and many conserved motif combinations at the C-terminal. We also detected many selection sites in these motif combinations. Expression analysis showed that Clade 1 genes had spatial and temporal differences and were highly expressed in various organs. The expression profile was closely related to the selection sites and motif combinations at the C-terminal. These observations represent essential entry points for revealing the functional differentiation of the SPL gene family. Our data presented here may provide a basis for future investigations of SPL genes in the Juglandaceae, especially for flower development and perhaps crop yield improvement.

Platycarya strobilacea leaf extract inhibits tumor necrosis factor-α production and bone loss induced by Porphyromonas gingivalis-derived lipopolysaccharide.

OBJECTIVE: Remodeling of alveolar bone is controlled by osteoclast-mediated bone resorption and osteoblast-induced bone formation. LPS of Porphyromonas gingivalis, a major causative agent of periodontitis, produces proinflammatory cytokines in host immune cells, which thereby triggers osteoclastogenesis and leads to alveolar bone resorption. We investigated the anti-periodontitis potential of Platycarya strobilacea leaf extract (PLE), which is used as a traditional medicine in Asian countries. DESIGN: TNF-α levels in cell culture media were measured using a commercially available enzyme-linked immunosorbent assay kit. Osteoclast differentiation was observed by tartrate-resistant acid phosphatase staining, and the expression levels of osteoclastogenic genes were measured by quantitative real-time PCR. Bone-resorbing activity was confirmed by the resorption pit formation, gelatin zymographic, and the cathepsin K activity assays. Osteogenic differentiation was confirmed with an ALP activity assay and alizarin red S staining. RESULTS: PLE treatment inhibited the production of TNF-α in P. gingivalis LPS-stimulated RAW264.7 macrophages. In bone marrow-derived macrophages serving as osteoclast precursors, PLE treatment blocked RANKL-induced osteoclastogenesis and gene expression levels of the osteoclastogenic transcription factor NFATc1, DC-STAMP for osteoclast fusion, and cathepsin K for osteoclast activity. In addition, PLE treatment reduced the formation of resorption pits and the secretion of MMP 9 and cathepsin K from the differentiated osteoclasts. Furthermore, PLE treatment induced osteogenesis by increasing ALP activity and calcium content in preosteoblastic cells. CONCLUSION: PLE inhibits P. gingivalis LPS-induced TNF-α production and bone resorption and induces bone formation. PLE may be a beneficial agent to promote oral health by inhibiting periodontitis-induced alveolar bone loss.

[Mechanism of Platycarya strobilacea Sieb. et Zucc extract-induced methuosis in human nasopharyngeal carcinoma CNE1 and CNE2 cells].

OBJECTIVE: To study the effect of Platycarya strobilacea Sieb. et Zucc (PSZ) extract on methuosis of human nasopharyngeal carcinoma CNE1 and CNE2 cells and explore the underlying mechanism. METHODS: CNE1 and CNE2 cells were treated with 1 mg/mL PSZ extract and the expressions of Rac1 mRNA and Rac1 protein were detected using RT-qPCR and Western blotting, respectively. Results CNE1 and CNE2 cells showed obvious morphological changes typical of methuosis following treatment with PSZ extract characterized by cell merging, accumulation of large cytoplasmic vacuoles, and membrane rupture without obvious changes in the nuclei. PSZ treatment resulted in up-regulated Rac1 mRNA and Rac1 protein expressions in the cells. Application of EHT 1864 obviously blocked the effect of PSZ extract in inducing methuosis in CNE1 and CNE2 cells. CONCLUSION: PSZ extract can induce methuosis in CNE1 and CNE2 cells by inducing the overexpression of Rac1.

Conservation genetics of Annamocarya sinensis (Dode) Leroy, an endangered endemic species.

The endangered perennial plant Annamocarya sinensis (Dode) Leroy is a tertiary relict tree restricted to southeastern China and northern Vietnam. To explore endangerment mechanisms, develop protection strategies, and guide reintroduction efforts for this species, we investigated genetic diversity and population structure by surveying 70 individuals from three distinct populations using 12 polymorphic microsatellite markers. We found high genetic diversity for A. sinensis as indicated by high allelic diversity (allelic number = 4.667 ± 0.436, effective number of alleles = 2.913 ± 0.249), excess heterozygosity (observed heterozygosity = 0.586 ± 0.039, expected heterozygosity = 0.582 ± 0.029), and low fixation index (-0.028 ± 0.057). Our research revealed low genetic differentiation (FST = 0.066 ± 0.011) and no correlation between genetic distance and geographic distance. Analysis of molecular variance attributed 87% of the variance to differences within the population, whereas 13% was distributed among populations. The protection strategy should aim to protect as many populations as possible. Promoting sexual reproduction among various genotypes and establishing an outcrossing program are advisable for A. sinensis.

[Phenotypic diversity of natural Cyclocarya paliurus populations seed traits].

With the seeds from nine natural Cyclocarya paliurus populations as test materials, their phenotypic traits, including 1000-seed weight, seed size, seed diameter, seed thickness, and seed diameter/thickness ratio, were investigated, and the phenotypic diversity among and within the populations were studied by the methods of ANOVA analysis, hierarchical cluster analysis, and correlation analysis. Significant differences were observed in the 1000-seed weight, seed size, seed diameter, and seed thickness among and within the populations, and in the seed diameter/thickness ratio within the populations, illustrating that there existed high phenotypic diversity of seed traits at these two levels. The mean phenotypic differentiation coefficient (V) of test seed traits was 20.54%, i. e., the variation among the populations was far smaller than that (79.46%) within the populations. The seed traits had different correlation degrees with geographical factors, and most affected by mean annual air temperature. According to the hierarchical cluster analysis based on the Euclidean distance, the nine natural Cyclocarya paliurus populations could be classified into three groups.

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets.

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.