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Aim Understanding how spatial distributions of rare and common species are associated with environmental and spatial processes is essential to understanding community assembly. We addressed the following questions: (a) does the relative importance of space and topography vary from rare to common tree species? (b) Are the contributions of topography and space equal? (c) Are the variances explained by topography or space correlated with elevational ranges (ER) at the local scale? (d) Does cell‐size influence those postulated associations? Location China and the Americas. Major taxa studied Tree species. Methods We partitioned the variation in species richness and composition of rare and common tree species by topography and space across a range of extents and grain sizes in eight communities. We calculated contribution ratio (CR) between space and topography to quantify their relative importance. We employed Kendall's rank correlation to determine the relation between CR and commonness. Mixed effect models were used to identify the influence of cell‐size on the results. Results The majority of CR values were positively related to increasing commonness, especially for composition. The explained variances by space were always higher than that by topography regardless of commonness. At local scale, variances explained by space or topography were not correlated with ER. Main conclusions Our results indicate that the relative importance of space compared to topography increases from rare to common species across forests. We suggest that future studies of community assembly need to account for both space and topography to adequately describe differences in rare and common species assembly mechanisms at range of spatial extents and grain sizes.

Elucidating the ecological mechanisms underlying community assembly in subtropical forests remains a central challenge for ecologists. The assembly of species into communities can be due to interspecific differences in habitat associations, and there is increasing evidence that these associations may have an underlying phylogenetic structure in contemporary terrestrial communities. In other words, by examining the degree to which closely related species prefer similar habitats and the degree to which they co-occur, ecologists are able to infer the mechanisms underlying community assembly. Here we implement this approach in a diverse subtropical tree community in China using a long-term forest dynamics plot and a molecular phylogeny generated from three DNA barcode loci. We find that there is phylogenetic signal in plant-habitat associations (i.e. closely related species tend to prefer similar habitats) and that patterns of co-occurrence within habitats are typically non-random with respect to phylogeny. In particular, we found phylogenetic clustering in valley and low-slope habitats in this forest, indicating a filtering of lineages plays a dominant role in structuring communities in these habitats and we found evidence of phylogenetic overdispersion in high-slope, ridge-top and high-gully habitats, indicating that distantly related species tended to co-occur in these high elevation habitats and that lineage filtering is less important in structuring these communities. Thus we infer that non-neutral niche-based processes acting upon evolutionarily conserved habitat preferences explain the assembly of local scale communities in the forest studied.

Objectives Castanopsis is the third largest genus in the Fagaceae family and is essentially tropical or subtropical in origin. The species in this genus are mainly canopy-dominant trees, and the key components of evergreen broadleaved forests play a crucial role in the maintenance of local biodiversity. Castanopsis chinensis , distributed from South China to Vietnam, is a representative species. It currently suffers from a high disturbance of human activity and climate change. Here, we present its assembled genome to facilitate its preliminary conservation and breeding on the genome level. Data description The C . chinensis genome was assembled and annotated by Nanopore and MGI whole-genome sequencing and RNA-seq reads using leaf tissues. The assembly was 888,699,661 bp in length, consisting of 133 contigs and a contig N50 of 23,395,510 bp. A completeness assessment of the assembly with Benchmarking Universal Single-Copy Orthologs (BUSCO) indicated a score of 98.3%. Repetitive elements comprised 471,006,885 bp, accounting for 55.9% of the assembled sequences. A total of 51,406 genes that coded for 54,310 proteins were predicted. Multiple databases were used to functionally annotate the protein sequences.

Objectives Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly. Data description This work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads using E. fordii leaf tissues. The de novo assembly contained 864,825,911 bp in the E. fordii genome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes ( rbcL , matK , ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.

Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny. We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot. The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.

Ormosia formosana is an important hardwood species and its seeds are popular as decorative jewelry. Currently, this species is threatened in the natural forests due to habitat destruction. Here, we first report the chloroplast genome of O. formosana for future studies in ecology, phylogeny, and conservation. The chloroplast genome of O. formosana is 173,587 bp in length with a GC content of 35.80%. It includes a large single-copy region of 73,550 bp, a small single-copy region of 18,683 bp, and two inverted repeat regions of 40,696 bp and 40,658 bp, respectively. The genome was totally annotated with 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis indicated that O. formosana is most genetically similar to O. boluoensis.

In general, even within a local area, many common plant species are found in different types of environment. We propose that if the association of a common plant species with different types of environment is investigated, by analysing all individuals in a given population as a single entity, the results might be misleading or incomplete owing to intraspecific variation. To test this hypothesis, we used molecular markers to classify mature Castanopsis chinensis individuals with a diameter at breast height ≥ 40 cm into different genetic groups and analysed the associations of these groups with topographic features and habitats within a 20-ha Dinghushan forest plot, South China. Our results indicated that the different groups had different topographical associations, and that the spatial distributions and genetic structures of individuals varied among the groups. Therefore, if significant genetic structure exists in the population of a common species within a community, to understand the relationship between the spatial distributions of individuals in the population and the environment, it is necessary to classify the individuals into genetic groups and analyse the data for these groups, rather than for a combined group of all individuals.

Global environmental changes drive biodiversity loss and community compositional change. Yet whether and how both factors simultaneously impact biomass dynamics in natural ecosystems remains elusive, especially considering their multidimensional effects (e.g., taxonomic, functional, and phylogenetic) over spatial scales. To fill this knowledge gap, we generated an experimental spatial gradient using circular quadrats that vary in radius (2–30 m) in a subtropical forest on Dinghushan Mountain, China. Within each quadrat over 10 years, we calculated the changes in aboveground biomass (i.e., net Δbiomass), biodiversity (i.e., Δbiodiversity for richness, Shannon diversity, functional, phylogenetic), and community composition (i.e., β-diversity for taxonomic, functional, phylogenetic). Based on multi-model inference, we determined the most parsimonious relationships of Δbiomass as a function of Δbiodiversity and β-diversity and then quantified their standardized coefficients in response to the spatial gradient. Our results showed that Δbiomass, Δbiodiversity, and β-diversity decreased with quadrat size; the former at an accelerating rate and the latter at decelerating rates. While Δbiomass as a function of Δbiodiversity and β-diversity had low occurrences across the gradient, Δbiomass was strongly related to the change in functional dispersion (i.e., ΔFDis) and taxonomic β-diversity at larger spatial scales. Our results suggest scale-dependent influences of biodiversity loss and community compositional change on biomass dynamics in natural ecosystems. Further, our results highlight that multiple dimensions of biodiversity should be considered when predicting biomass dynamics at large spatial scales.

Environmental filtering and competitive interactions are important ecological processes in community assembly. The contribution of the two processes to community assembly can be evaluated by shifts in functional diversity patterns. We examined the correlations between functional diversity of six traits (leaf chlorophyll concentration, dry matter content, size, specific leaf area, thickness and wood density) and environmental gradients (topography and soil) for 92 species in the 20-ha Dinghushan forest plot in China. A partial Mantel test showed that most of the community-weighted mean trait values changed with terrain convexity and soil fertility, which implied that environmental filtering was occurring. Functional diversity of many traits significantly increased with increasing terrain convexity and soil fertility, which was associated with increased light and below-ground resources respectively. These results suggest that co-occurring species are functionally convergent in regions of strong abiotic stress under the environmental filtering, but functionally divergent in more benign environments due to resource partitioning and competitive interactions. Single-trait diversity and multivariate functional diversity had different relationships with environmental factors, indicating that traits were related to different niche axes, and associated with different ecological processes, which demonstrated the importance of focusing niche axes in traits selection. Between 9% and 41% of variation in functional diversity of different traits was explained by environmental factors in stepwise multiple regression models. Terrain convexity and soil fertility were the best predictors of functional diversity, which contributed 30.5% and 29.0% of total R2 to the model. These provided essential evidence that different environmental factors had distinguishing impacts on regulating diversity of traits.