Niche convergence and biogeographic history shape elevational tree community assembly in a subtropical mountain forest.

Niche convergence or conservatism have been proposed as essential mechanisms underlying elevational plant community assembly in tropical mountain ecosystems. Subtropical mountains, compared to tropical mountains, are likely to be shaped by a mixing of different geographic affinities of species and remain somehow unclear. Here, we used 31 0.1-ha permanent plots distributed in subtropical forests on the eastern and western aspects of the Gaoligong Mountains, southwest China between 1498 m and 3204 m a.sl. to evaluate how niche-based and biogeographic processes shape tree community assembly along elevational gradients. We analyzed the elevational patterns of taxonomic, phylogenetic and functional diversity, as well as of individual traits, and assessed the relative importance of environmental effects on these diversity measures. We then classified tree species as being either tropical affiliated or temperate affiliated and estimated their contribution to the composition of biogeographic affinities. Species richness decreased with elevation, and species composition showed apparent turnover across the aspects and elevations. Most traits exhibited convergent patterns across the entire elevational gradient. Phylogenetic and functional diversity showed opposing patterns, with phylogenetic diversity increasing and functional diversity decreasing with elevation. Soil nutrients, especially phosphorus and nitrogen, appeared to be the main abiotic variables driving the elevational diversity patterns. Communities at lower elevations were occupied by tropical genera, while highlands contained species of tropical and temperate biogeographic affinities. Moreover, the high phylogenetic diversity at high elevations were likely due to differences in evolutionary history between temperate and tropical species. Our results highlight the importance of niche convergence of tropical species and the legacy of biogeographic history on the composition and structure of subtropical mountain forests. Furthermore, limited soil phosphorus caused traits divergence and the partitioning for different forms of phosphorus may explain the high biodiversity found in phosphorus-limited subtropical forests.

The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP).

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.

Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata).

Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.

Seed Germination and Seedling Growth Influenced by Genetic Features and Drought Tolerance in a Critically Endangered Maple.

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47-76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

Does the critically endangered Rhododendron amesiae deserve top priority for conservation?

1.If a threatened plant has the problem of inaccurate species delimitation, its conservation programs that have previously been implemented might be debated.2.We made a comprehensive comparison of the critically endangered R. amesiae and its close relative R. concinnum, employing both morphological and population genomic data (ddRAD-seq).3.We suggest that the critically endangered R. amesiae can be merged into R. concinnum. Hence, the threatened status of R. amesiae is needed to be reevaluated.

Unusual patterns of hybridization involving two alpine Salvia species: Absence of both F1 and backcrossed hybrids.

Natural hybridization plays an important role in speciation; however, we still know little about the mechanisms underlying the early stages of hybrid speciation. Hybrid zones are commonly dominated by F1s, or backcrosses, which impedes further speciation. In the present study, morphological traits and double digest restriction-site associated DNA sequencing (ddRAD-seq) data have been used to confirm natural hybridization between Salvia flava and S. castanea, the first case of identification of natural hybridization using combined phenotypic and molecular evidence in the East Asian clade of Salvia. We further examined several reproductive barriers in both pre-zygotic and post-zygotic reproductive stages to clarify the causes and consequences of the hybridization pattern. Our results revealed that reproductive isolation between the two species was strong despite the occurrence of hybridization. Interestingly, we found that most of the hybrids were likely to be F2s. This is a very unusual pattern of hybridization, and has rarely been reported before. The prevalence of geitonogamy within these self-compatible hybrids due to short distance foraging by pollinators might explain the origin of this unusual pattern. F2s can self-breed and develop further, therefore, we might be witnessing the early stages of hybrid speciation. Our study provides a new case for understanding the diversification of plants on the Qinghai-Tibet Plateau.

The complete chloroplast genome of Acer Pubipetiolatum var. pingpienense (Sapindaceae).

The genus Acer is widespread throughout the northern temperate zone, and many species within the genus are of ecological and economical importance. Here we report the newly sequenced chloroplast genome of Acer pubipetiolatum var. pingpienense. This chloroplast genome has a total length of 156,730 bp, and contains a pair of inverted repeats (IRs, 26,743 bp), a large single-copy (LSC) region of 71,582 bp and a small single-copy (SSC) region of 18,092 bp. Phylogenetic analysis suggests that A. pubipetiolatum var. pingpienense is closely related to A. laevigatum, and both fall into Section Palmata. The complete A. pubipetiolatum var. pingpienense chloroplast genome will provide an important genetic resource for future research into the conservation and evolution of this genus. Our findings also suggest that further research is necessary to elucidate the phylogenetic relationships between plant species within this genus.

Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.

Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne ) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.

Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan (China), based on morphological and genomic data.

Rhododendron kuomeianum Y.H. Chang, J. Nielsen & Y.P. Ma, a new species of Rhododendron (Ericaceae) within subsect. Maddenia in sect. Rhododendron from Yiliang County, NE Yunnan, China, is described and illustrated. The new species is similar to R. valentinianum, but it can be easily distinguished by its sparse scales on the abaxial surface of the leaf blade, fewer flowers per inflorescence and white corolla with pale red margins. There are also differences in the widths of calyx lobes, leaf blade shape and indumentum characteristics of the petiole between the new species and Rhododendron linearilobum. We confirmed that R. kuomeianum is a new species closely related to R. valentinianum and R. changii with phylogenomic studies of 10 species within this subsection based on restriction site-associated DNA sequencing (RAD-seq) data. These phylogenomic analyses also clarified additional taxonomic problems in this subsection previously raised by morphological analysis. Our findings make a strong case for using next-generation sequencing to explore phylogenetic relationships and identify new species, especially in plants groups with complicated taxonomic problems.

Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation.

Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations.

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H E  = 0.0742 ± 0.002). Both F ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs.

Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima's D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, H e = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (F st from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (N e ) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of N e over a short period, and a subsequent gradual decline in N e to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.

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Plant diversity monitoring is an essential basis for plant conservation and policy making, and is critical to the sustainable use and protection of biological resources. We reviewed the research progress on plant diversity monitoring, and proposed further research direction. Plant diversity monitoring is developing rapidly at a new situation, and enters a new era referring to intelligent, integration of macroscopic and microscopic, networked monitoring, big data, large-scale, multidisciplinary, all-dimensional, from species level to family level, community level or ecosystem level, and even the global level. The construction of biodiversity monitoring network promotes the uniform of essential biodiversity variables and networked monitoring. Internet information and database had become a main data source of plant diversity. There are many new challenges in plant diversity monitoring, including standardization, effective utilization and sharing of the monitoring data, as well as the monitoring for genetic diversity and individuals. Ecological monitoring would be large-scale, automated and standardized. Many things should be addressed in further research, including to improve the monitoring networks, to find innovative ways and build new models, to carry out monitoring at hotspots and give priority to important species as well as community or even larger scale, to pay more attention to the background investigation of plant resource.

The complete chloroplast genome of Berchemia lineata, an important medicinal plant from China.

Brechemia lineata is a well-known medicinal plant in the Rhamnaceae family and widely used in traditional Chinese medicine. Here, we sequenced the complete chloroplast genome using Illumina pair-end sequencing data. The chloroplast genome was 154,962 bp in length, consisting of a large single-copy (LSC) region of 82,928 bp, a small single-copy (SSC) region of 17,376 bp, and a pair of inverted repeat (IR) regions of 27,329 bp. The chloroplast genome consists of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes. The overall GC content of the chloroplast genome was 37.0%. The phylogenetic analysis suggests close relationship of B. lineata with other Berchemia species. These genomic resources will be valuable resource for systematic and phylogenetic studies of Berchemia genus.

Complete plastid genome of Rhododendron griersonianum, a critically endangered plant with extremely small populations (PSESP) from southwest China.

The complete plastid genome of Rhododendron griersonianum, a critically endangered plant species with extremely small populations, was obtained using Illumina HiSeq X Ten and ONT PromethION sequencing. The full length of the plastid genome is 206,467 bp with an overall GC content of 35.8%, which encodes 118 unique genes, including 78 protein-coding genes, 36 tRNA and 4 rRNA genes. Phylogenetic analysis revealed that all Rhododendron species formed a monophyletic clade. This study provides a valuable reference and will facilitate future studies related to the general characteristics and evolution of plastid genomes in the genus Rhododendron.

Ceropegia jinshaensis (Apocynaceae), a new species from northwestern Yunnan, China.

Ceropegia jinshaensis D.T.Liu & Z.K.Wu (Asclepiadoideae, Apocynaceae), a new species from northwestern Yunnan along the upper Yangtze river of China, is described and illustrated. This species is similar to C. meleagris H. Huber, C. dorjei C. E. C. Fischer and C. aridicola W. W. Smith, but can be distinguished easily by its leaf shape and floral features, especially the corolla shape and size, the interior of corolla tube and coronal characters.

Two new species of Henckelia (Gesneriaceae) from Southeastern Yunnan, China.

Two new species of Gesneriaceae, Henckelia nanxiheensis Lei Cai & Z.L.Dao, sp. nov. and H. multinervia Lei Cai & Z.L.Dao, sp. nov. from southeastern Yunnan, China, are described with color photos. The diagnostic characters of the two new species, together with photographs, detailed descriptions, distribution and habitat, as well as comparisons with morphologically similar species, are also provided.

Biodiversity explains maximum variation in productivity under experimental warming, nitrogen addition, and grazing in mountain grasslands.

Anthropogenic global warming, nitrogen addition, and overgrazing alter plant communities and threaten plant biodiversity, potentially impacting community productivity, especially in sensitive mountain grassland ecosystems. However, it still remains unknown whether the relationship between plant biodiversity and community productivity varies across different anthropogenic influences, and especially how changes in multiple biodiversity facets drive these impacts on productivity. Here, we measured different facets of biodiversity including functional and phylogenetic richness and evenness in mountain grasslands along an environmental gradient of elevation in Yulong Mountain, Yunnan, China. We combined biodiversity metrics in a series of linear mixed-effect models to determine the most parsimonious predictors for productivity, which was estimated by aboveground biomass in community. We examined how biodiversity-productivity relationships were affected by experimental warming, nitrogen addition, and livestock-grazing. Species richness, phylogenetic diversity, and single functional traits (leaf nitrogen content, mg/g) represented the most parsimonious combination in these scenarios, supporting a consensus that single-biodiversity metrics alone cannot fully explain ecosystem function. The biodiversity-productivity relationships were positive and strong, but the effects of treatment on biodiversity-productivity relationship were negligible. Our findings indicate that the strong biodiversity-productivity relationships are consistent in various anthropogenic drivers of environmental change.