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The coexistence of closely related species is key to understanding the nature of biodiversity hotspots where in situ diversification has yielded rich communities of close relatives. Limiting similarity predicts that co‐occurring species are differentiated in their niches; identifying the axes of differentiation in sympatric close relatives can thus help reveal the eco‐evolutionary dynamics of community assembly. For flowering plants, these axes may be temporal (related to reproductive phenology) or morphological (related to functional traits).We collected fine‐scale data on abundance, morphology and phenology over a flowering season for 34 species of Rhododendron (Ericaceae) spanning a 2700 m elevation gradient in a nature reserve in the eastern Hengduan Mountains, China. We used null models to test for patterns of clustering versus overdispersion in species' abundances, phylogenetic relatedness and functional traits across sites, and applied joint distribution models to examine the correlates of pairwise associations.We found that species tended to be spatially aggregated, indicating that communities are not strongly structured by competitive exclusion. At higher elevation sites, species tended to be vegetatively more similar (clustered) and closely related. Environmental variables, including climate and topography, were strong predictors of species' ranges. No evidence of niche differentiation was detected along spatial or morphological (functional) axes, but along the temporal axis, the phenology of co‐occurring species showed significant divergence, and was less phylogenetically conserved compared to morphological traits.Synthesis. Local communities of Rhododendron in its centre of diversity are structured by environmental filtering and the effects of limiting similarity. Evidence for the latter is apparent in the pervasive phenological divergence of co‐occurring species, likely driven by reproductive interference from shared pollinators. The evolutionary lability of flowering time appears to render it the quickest path to coexistence for recently diverged species that experience secondary contact in this biodiversity hotspot. [ABSTRACT FROM AUTHOR]

Carpinus (Betulaceae) has approximately 52 species distributed in the Northern Hemisphere, with many species of Carpinus found in China. However, the species boundaries and phylogenetic relationships remain poorly understood. This study reported ITS sequences for 225 individuals of 33 Carpinus species, mainly from China. We also included eight Ostrya species in our analyses, the closely related sister group of Carpinus. We aimed to delimit these species based on ITS sequences and clarify their phylogenetic relationships by constructing tree-like topology and networks at population level. We found that only 17 of 33 species could be delimited from the closely related ones based on species-specific mutations in ITS sequence variation, including all species of sect. Distegocarpus , and sect. Carpinus subsect. Carpinus. Carpinus subsect. Carpinus contained two endangered species, although one seemed to be a recently originated allopolyploid species with genetic additivity from two likely parents in the ITS sequence variation. Sixteen species of sect. Carpinus subsect. Polyneurae were classified into three species complexes, in each of which two or more could be not distinguished from each other. The closely related species of these complexes may still diverge at the early stage without genetic distinction in the nuclear ITS sequences because of too short of divergence time and frequent gene flow. Otherwise, some species may be established based on the intraspecific variations without genetic bases for an independently evolving unit. [ABSTRACT FROM AUTHOR]

Delimitating species boundaries is the primary aim of biological classification and could be critical for evaluating the evolving process of species and conserving biodiversity. Rhododendron is an iconic group with an extraordinary diversity in southwest China. However, it remains unknown whether the recorded species therein comprise independently evolving lineages or artificially delimitated morphological entities. In this study, we carried out species delimitation of four Rhododendron species in the R. vernicosum - R. decorum species complex based on morphological analyses and population genetic data from nuclear simple sequence repeats (SSR) markers. We randomly selected a total of 105 specimens of different individuals identified as four species across their distributional ranges to examine the statistically distinct phenotypic clusters based on 19 morphological traits. Similarly, we genotyped 55 individuals of four species from 21 populations using 15 SSR markers. The morphological analyses sorted R. decorum and the other three species into two different phenotypic clusters. The genetic clusters were consistent with the morphological clusters. However, we also recovered the third genetic cluster, comprising six R. vernicosum populations and containing the admixed genetic compositions of the other two distinct genetic clusters. This hybrid group was morphologically similar to the typical R. vernicosum (including the samples from its type specimen locality and both R. verruciferum and R. gonggashanense) but with more genetic ancestry from R. decorum. Based on our findings, we identify two distinct species and one putative hybrid group due to introgression in the R. vernicosum-R. decorum species complex. We propose to merge R. verruciferum and R. gonggashanense into R. vernicosum based on genetic compositions and our morphological analyses. The hybrid group inferred from our findings, however, needs further investigations. [ABSTRACT FROM AUTHOR]

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago , eight Trigonella , and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA , trnK-matK , and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera. [ABSTRACT FROM AUTHOR]

Megacarpaea delavayi (Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000–4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome of M. delavayi is 883 Mb, and 61.59% of the genome is composed of repeat sequences. Annotation of the genome identified a total of 41,114 protein-coding genes. We found that M. delavayi experienced an independent whole-genome duplication (WGD), paralleling those independent WGDs in Iberis , Biscutella , and Anastatica in the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genus Megacarpaea within the expanded lineage II of the family and resolved its basal divergence to a subclade consisting of Anastatica, Iberis , and Biscutella. Species-specific and fast-evolving genes in M. delavayi are mainly involved in "DNA repair" and "response to UV-B radiation." These genetic changes may together help this species survive in high-altitude environments. The reference genome reported here provides a valuable resource for studying adaptation of this and other alpine plants to the high-altitude habitats. [ABSTRACT FROM AUTHOR]

Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments ( trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer ( ITS) region for all samples. Sequence variations of Ostrya from four cp DNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants. [ABSTRACT FROM AUTHOR]

• Because of heterogeneous topographies, high-mountain areas could harbor a significant pool of cryptic forest refugia (glacial microrefugia unrecognized by palaeodata), which, as a result of poor accessibility, have been largely overlooked. The juniper forests of the southern Tibetan Plateau, with one of the highest tree lines worldwide, are ideal for assessing the potential of high-mountain areas to harbor glacial refugia. • Genetic evidence for Last Glacial Maximum (LGM) endurance of these microrefugia is presented using paternally inherited chloroplast markers. Five-hundred and ninety individuals from 102 populations of the Juniperus tibetica complex were sequenced at three polymorphic chloroplast regions. • Significant interpopulation differentiation and phylogeographic structure were detected ( GST = 0.49, NST = 0.72, NST > GST, P < 0.01), indicating limited among-population gene flow. Of 62 haplotypes recovered, 40 were restricted to single populations. These private haplotypes and overall degrees of diversity were evenly spread among plateau and edge populations, strongly supporting the existence of LGM microrefugia throughout the present distribution range, partly well above 3500 m. • These results mark the highest LGM tree lines known, illustrating the potential significance of high-mountain areas for glacial refugia. Furthermore, as the close vicinity of orographic rear-edge and leading-edge populations potentially allows gene flow, surviving populations could preserve the complete spectrum of rear-edge and leading-edge adaptations. [ABSTRACT FROM AUTHOR]

This paper provides information about the distribution, structure, and ecology of the world's largest alpine ecosystem, the Kobresia pygmaea pastures in the southeastern Tibetan plateau. The environmental importance of these Cyperaceae mats derives from the extremely firm turf, which protects large surfaces against erosion, including the headwaters of the Huang He, Yangtze, Mekong, Salween, and Brahmaputra. The emphasis of the present article is on the climate-driven evolution and recent dynamics of these mats under the grazing impact of small mammals and livestock. Considering pedological analyses, radiocarbon datings, and results from exclosure experiments, we hypothesize that the majority of K. pygmaea mats are human-induced and replace forests, scrub, and taller grasslands. At present, the carrying capacity is increasingly exceeded, and reinforced settlement of nomads threatens this ecosystem especially in its drier part, where small mammals become strong competitors with livestock and the removal of the turf is irreversible. Examples of rehabilitation measures are given. [ABSTRACT FROM AUTHOR]

An inventory of isolated tree stands surrounded by desert pastures in Southern Tibet (A.R. Xizang, China) revealed more than 50 sites with vigorous trees of Juniperus convallium Rehder & E.H. Wilson and Juniperus tibetica Kom and additional more than 10 records where juniper trees had been destroyed between 1959–1976. The tree stands are not restricted to any specific habitat, and occur within an area stretching 650 km westwards from the current forest border of Southern Tibet. The trees are religious landmarks of the Tibetan Buddhists. The highest trees were found at an elevation of 4,860 m. Vegetation records, rainfall correlations and temperature data collected by local climate stations and successful reforestation trials since 1999 indicate that forest relicts fragmented through human interference could regenerate if current cattle grazing and deforestation practices are halted. The drought line of Juniperus forests in Southern Tibet is approximately 200–250 mm/a. A first pollen diagram from Lhasa shows forest decline associated with the presence of humans since at least 4,600 yr BP. The currently degraded commons developed in the last 600 yr. To date, no findings of remains of ancient forests in the Central Tibetan Highlands of the Changtang have been reported. [ABSTRACT FROM AUTHOR]

Numbers and sizes of photovoltaic solar power plants have grown unprecedentedly over the last few years in China, which aims to achieve a carbon emission peak by 2030 and carbon neutrality by 2060. Thus, timely and accurate monitoring of photovoltaic solar power plants is crucial to the design and management of renewable electricity systems in China. Random forest algorithm has been used to map photovoltaic solar power plants at multiple scales, however, it always causes several salt-and-pepper noises, limiting its application at larger spatial scales. Here we first develop a photovoltaic solar power plant mapping method through integrating time series Landsat imagery, random forest, and morphological characteristics. Then we apply this method in Gansu Province, which has abundant solar and wind energy resources and provide large amounts of potential lands for photovoltaic development, and generate the annual photovoltaic maps from 2015 to 2020. We further analyze the spatial-temporal dynamics of sizes and areas of photovoltaic solar power plants and major land cover conversion of expansive photovoltaic regions. Finally, we discuss the reliability, uncertainties, implications, and future development of our improved methods. We find our photovoltaic mapping method can remove most of salt-and-pepper noises effectively, and the resultant maps in Gansu for 2020 have very high accuracies with user's and producer's accuracies of 97.57% and 99.22%, respectively. There are 165.29 km2 photovoltaic solar power plants in Gansu for 2020, and most of which are located in the northwestern Gansu. In addition, the photovoltaic with patch size > 1 km2 and ≤ 2 km2 (53.4 km2, 32.3%) has largest patch number (39, 15.7%). The improved photovoltaic mapping methods and further analysis in this study provide critical information for accurate and automatic classification of photovoltaic solar power plants in the future, as well as the environmental and sustainable development of solar energy in China. • Improved random forest mapping algorithm of photovoltaic solar power plants. • An updated annual map of photovoltaic solar power plants in Gansu Province with improved accuracy. • Detailed spatial-temporal dynamics and major land cover conversion of photovoltaic solar power plants in Gansu. [ABSTRACT FROM AUTHOR]

Gentiana straminea is a popular Tibetan medicine that has been used for thousands of years in China to treat various diseases and conditions. Although it has multiple pharmaceutical purposes and important economic plant resource in China, transcriptome and molecular base still known limited. In flowering season, samples were collected from different tissues, using the NGS Illumina. Solexa platform, about 58.85 million sequencing reads were generated and assembled de novo, yielding 78,764 high quality unigenes with an average length of 1090 bp. Gene Ontology (GO), KEGG pathway mapping showed that 49,033 of these were identified as putative homologs of annotated sequences in the protein databases. Among them, candidate genes associated with iridoid, flavonoid and anthocyanin were identified. Further the key enzymes involved to iridoid and flavonoid synthesis pathway were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) on different tissues, the flower and root had the higher expression than leaves. In addition, 7591 SSR markers were identified from the unigenes of the G . straminea transcriptome. The foundation of G . straminea provided the important resource for facilitating to study molecular and functional genomics of it and related this species on the Qinghai–Tibet Plateau. [ABSTRACT FROM AUTHOR]

Relationships between biodiversity and multiple ecosystem functions (that is, ecosystem multifunctionality) are context-dependent. Both plant and soil microbial diversity have been reported to regulate ecosystem multifunctionality, but how their relative importance varies along environmental gradients remains poorly understood. Here, we relate plant and microbial diversity to soil multifunctionality across 130 dryland sites along a 4,000 km aridity gradient in northern China. Our results show a strong positive association between plant species richness and soil multifunctionality in less arid regions, whereas microbial diversity, in particular of fungi, is positively associated with multifunctionality in more arid regions. This shift in the relationships between plant or microbial diversity and soil multifunctionality occur at an aridity level of ∼0.8, the boundary between semiarid and arid climates, which is predicted to advance geographically ∼28% by the end of the current century. Our study highlights that biodiversity loss of plants and soil microorganisms may have especially strong consequences under low and high aridity conditions, respectively, which calls for climate-specific biodiversity conservation strategies to mitigate the effects of aridification., (© 2021. The Author(s).)

Many plant species comprising the present-day Arctic flora are thought to have originated in the high mountains of North America and Eurasia, migrated northwards as global temperatures fell during the late Tertiary period, and thereafter attained a circumarctic distribution. However, supporting evidence for this hypothesis that provides a temporal framework for the origin, spread and initial attainment of a circumarctic distribution by an arctic plant is currently lacking. Here we examined the origin and initial formation of a circumarctic distribution of the arctic mountain sorrel (Oxyria digyna) by conducting a phylogeographic analysis of plastid and nuclear gene DNA variation. We provide evidence for an origin of this species in the Qinghai-Tibet Plateau of southwestern China, followed by migration into Russia c. 11 million yr ago (Ma), eastwards into North America by c. 4 Ma, and westwards into Western Europe by c. 1.96 Ma. Thereafter, the species attained a circumarctic distribution by colonizing Greenland from both sides of the Atlantic Ocean. Following the arrival of the species in North America and Europe, population sizes appear to have increased and then stabilized there over the last 1 million yr. However, in Greenland a marked reduction followed by an expansion in population size is indicated to have occurred during the Pleistocene., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

Background and Aims: Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance., Methods: Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome., Key Results: In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor-derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence., Conclusions: The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.

Population genetics data based on multiple nuclear loci provide invaluable information to understand demographic, selective, and divergence histories of the current species. We studied nucleotide variation at 13 nuclear loci in 53 populations distributed among four closely related, but morphologically distinct juniper species of the Qinghai-Tibetan Plateau (QTP). We used a novel approach combining Approximate Bayesian Computation and a recently developed neutrality test based on the maximum frequency of derived mutations to examine the demographic and selective histories of individual species, and isolation-with-migration analyses to study the joint history of the species and detect gene flow between them. We found that (1) the four species, which diverged in response to the extensive QTP uplifts, have different demographic histories; (2) two loci, Pgi and CC0822, depart significantly from neutrality in one species and Pgi, is also marginally significant in another; and (3) shared polymorphisms are common, indicating both incomplete lineage sorting and gene flow after species divergence. In addition, the detected unidirectional gene flow provides indirect support for the theoretical prediction that introgression should mostly take place from local to invading species. Our results, together with previous studies, underscore complex evolutionary histories of plant diversification in the biodiversity-hotspot QTP., (© 2011 The Author(s). Evolutiona© 2011 The Society for the Study of Evolution.)

Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.

Background: Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population level through phylogeographic analysis. Here we report such a case study on eight putative cypress (Cupressus) species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The analysis involved sequencing three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF) in 371 individuals sampled from populations at 66 localities., Results: Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure (N(ST) > G(ST), P < 0.05) implied a high correlation between haplotypes/lineages and geographic distribution. Two species, C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity., Conclusions: It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.

In many plant species, leaf morphology varies with altitude, an effect that has been attributed to temperature. It remains uncertain whether such a trend applies equally to juvenile and mature trees across altitudinal gradients in semi-arid mountain regions. We examined altitude-related differences in a variety of needle characteristics of juvenile (2-m tall) and mature (5-m tall) alpine spruce (Picea crassifolia Kom.) trees growing at altitudes between 2501 and 3450 m in the Qilian Mountains of northwest China. We found that stable carbon isotope composition (delta(13)C), area- and mass-based leaf nitrogen concentration (N(a), N(m)), number of stomata per gram of nitrogen (St/N), number of stomata per unit leaf mass (St/LM), projected leaf area per 100 needles (LA) and leaf mass per unit area (LMA) varied nonlinearly with altitude for both juvenile and mature trees, with a relationship reversal point at about 3100 m. Stomatal density (SD) of juvenile trees remained unchanged with altitude, whereas SD and stomatal number per unit length (SNL) of mature spruce initially increased with altitude, but subsequently decreased. Although several measured indices were generally found to be higher in mature trees than in juvenile trees, N(m), leaf carbon concentration (C(m)), leaf water concentration (LWC), St/N, LA and St/LM showed inconsistent differences between trees of different ages along the altitudinal gradient. In both juvenile and mature trees, delta(13)C correlated significantly with LMA, N(m), N(a), SNL, St/LM and St/N. Stomatal density, LWC and LA were only significantly correlated with delta(13)C in mature trees. These findings suggest that there are distinct ecophysiological differences between the needles of juvenile and mature trees that determine their response to changes in altitude in semi-arid mountainous regions. Variations in the fitness of forests of different ages may have important implications for modeling forest responses to changes in environmental conditions, such as predicted future temperature increases in high altitude areas associated with climate change.