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Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.

Additional file 5: Table S1. The results of neutrality tests (Tajima’s D and Fu’s FS tests) and mismatch distribution analyses.

Additional file 4: Fig. S4. Haplotypes network of Opisthopappus. 47 haplotypes (H1-H47) were detected in O. longilobus and 28 haplotypes (H48-H75) in O. taihangensis. No shared haplotypes were detected between O. longilobus and O. taihangensis. The color of each haplotype corresponded to Fig. 1 The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step.

Additional file 6: Table S2. ANOVA analysis for the nineteen bioclimatic variables grouped by two different species.

Additional file 3: Fig. S3 The Kruskal–Wallis test of the first two principal components and the first two linear discriminants of the genetic variation revealed significant genetic divergence between species but no or little population differentiation within species. (A–D): Comparisons between species. (E–H): Comparisons among populations.

Additional file 2: Fig. S2. Structure analysis from K = 3 to K = 6 for SNP and InDel, respectively.

Additional file 7: Fig. S5. The average temperature of every month (A) and the average precipitation of every month (B) of the studied populations of the distribution of Opisthopappus.

Additional file 8: Table S3. Information of primer pairs.

Additional file 1: Fig. S1. Phylogenetic relationships between O. longilobus and O. taihangensis. (A): Individual ML clustering of Opisthopappus. Blue branches presented individuals of O. longilobus and red branches presented individuals of O. taihangensis. (B): UPGMA clustering for 24 populations of Opisthopappus based on Nei’s genetic distance. Blue for populations of O. longilobus and red for populations of O. taihangensis.

Background Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated. Results Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains. Conclusions The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.

Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.

Background: Acer ginnala is a deciduous shrub/small tree that primarily distributed across the northern regions of China. It comprises a foundation species in many terrestrial ecosystems and has significant ornamental and economic value. Owing to its increased use as an economic resource, overexploitation and environmental destruction have resulted in the vulnerability of this species. Thus, the elucidation of the genetic differentiation and influence of environmental factors on A. ginnala is very critical for its management and future utilization strategies. Results: Our results revealed that high genetic variation occurred in A. ginnala species while low genetic diversity was observed at the population level. Most differentiation has found among populations. A significant correlation existed between genetic and environmental distances. Seven climate variables (bio1, bio2, bio3, bio4, bio13, bio15 and bio18) might explain the substantial levels of genetic variation (> 40%) in populations. The most suitable areas of this species appeared in Shaanxi, Shanxi, Anhui Provinces, and Northeastern China based on ENM results. Compared to the last interglacial (LIG) period, A. ginnala migrated toward Northern and Northeastern China, and extended to the most suitable areas during the last glacial maximum (LGM) period. Shanxi and Anhui Provinces might have served as refugium owing to their relatively high genetic variation. Conclusions: Low genetic diversity at the population level that may be the source of its vulnerability. Climate heterogeneity would play an important role in the pattern of genetic differentiation in A. ginnala populations. The A. ginnala population was isolated by a heterogeneous climate and subsequently began to adapt to local selection processes resulted in high genetic divergence.

The artificial neural network is attractive for ecological studies for its power in analyzing and solving complicated and nonlinear matters. The Self-Organizing Feature Map (SOFM) ordination were described and applied to the analysis of Taxus chinensis var. mairei forests in Shanxi province of China in this paper. The data matrix is the important values of 128 species in 95 quadrats. The results showed that SOFM ordination displayed forest communities in species space which reflected ecological gradients successfully. Its first axis is comprehensive gradient of topographical factors and its second axis is a comprehensive gradient of soil variables. SOFM ordination also distinguished 95 quadrats into eight forest types. SOFM ordination made the interpretation of relationships between communities, species, and environments easier.

The conservation of the endemic, endangered, and first-class protected tree species, Taxus chinensis var. mairei (Lem. & H. Lev.) W. C. Cheng & L. K. Fu, is urgent in China. To assist the protection of this important medicinal plant species, the biological and ecological characteristics of its populations were investigated and analyzed in Shanxi. The study area, southeastern Shanxi, is a special region suitable for this species growth and development. The floristic composition, life form spectrum, and species diversity of T. chinensis var. mairei forests reflected the features of both warm-temperate and subtropical regions. Size classes in DBH and static life table analysis showed that the population structure of T. chinensis var. mairei was of the increase-type. Plant density, survivorship, and mortality decreased with increase in age. Distribution patterns of individuals were basically clumped and saplings tended to be distributed randomly. Disturbance from collection of leaves, branches, and stems for medicine was an important factor affecting population structure, dynamics, and distribution. The sex ratio of female/male and the efficiency of sexual reproduction were very low. The main way of reproduction for this species is vegetative propagation. Based on these characteristics, some suggestions, such as establishing nature reserves, improving population structure by cultivation and transplantation, developing seed gardens, and plantations, etc., for the conservation management of T. chinensis var. mairei and its forests in Shanxi are discussed.

Paeonia suffruticosa var. spontanea, distributed in a very small area in Shanxi and Shaanxi provinces of China, is an endemic, endangered, and nationally protected species. To assist the protection of this species, the biological and ecological characteristics of its populations were investigated and analyzed. There are eight communities (TWINSPAN result) in which this species is found. It prefers forest communities dominated by Quercus liaotungensis in the warm-temperate climate zone. Its spatial distribution pattern is clumped in all communities. Its populations are expanding in all study areas. Biomass and productivity are closely related to plant age, density, and environmental conditions. The level of sexual reproduction is low, and the main method of reproduction of this species is vegetative propagation. Canopy gaps may be important for the establishment, growth, and reproduction of this species. Based on these characteristics, some suggestions for the conservation management of Paeonia su...

The Loess Plateau is one of the most environmentally sensitive regions in China. This study addresses the relationships between vegetation and climate of this area quantitatively at a large-scale, in order to determine the factors that control vegetation distribution. The Loess Plateau, located at 101°01′–155°10′ E and 34°02′–40°40′ N, covers an area of 52 million hectares. Vegetation data were collected from the vegetation map (1:500,000) and the Landsat Thematic Mapper scenes of the Loess Plateau. The Loess Plateau was divided into small districts of 30′ latitude by 30′ longitude on the vegetation map. In each district, areas with different vegetation were measured and used as vegetation data. The climatic data were average values of county meteorological records in each district in the past 25 years. GIS, TWINSPAN and canonical correspondence analysis (CCA) were employed for analysis. 257 small districts were clustered into 7 groups using TWINSPAN, representing 7 vegetation regions or subregions. The first three CCA axes had significant correlations with climate. The first CCA axis represented the variation of vegetation and climate along the latitude gradient, while the second CCA axis the variation along the longitude gradient. The distribution pattern of 171 vegetation formations on the CCA plot is identical to that of vegetation regions (districts). The spatial distribution of vegetation is closely related to climate variables on the Loess Plateau. Water variables and temperature are important in both latitude and longitude gradients, while the sunshine hours, accumulated temperature and wind speed are more important than water variables and temperature in longitude gradients.

Artificial neural network is powerful in analyzing and solving complicated and non-linear matters. SOFM (self-organizing feature map) clustering was described and applied to the analysis of woodland communities in the Guancen Mountains of China. The dataset was consisted of importance values of 112 species in 53 quadrats. SOFM clustering classified the 53 quadrats into eight groups, representing eight associations of vegetation. These results are ecologically meaningful, which suggests that SOFM clustering is effective method in studies of ecology.

Lishan Mountain is belonged to the Zhongtiao Ranges in Southeast Shanxi, and situated between 35 degrees 16'30" - 35 degrees 27'20" N and 111 degrees 51'-- 112 degrees 5'35" E. The climate is cool and arid in winter, but warm and rainy in summer. This paper studied the species diversity and community structure of forest communities there, based on field investigation data and by using diversity, richness and evenness indices. The results showed that the species diversity and evenness of the communities were in the order of Acer davidii + Acer monoAcer davidii + Carpinus turczaninouiiQuercus liaolugensisQuercus varibilisPinus armandii + Betula albo-sinensisPinus tabulaeformis + Quercus glanduliferaBetula platyphyllaPlatycladus orientalis + Quercus variabilisBetula albo-sinensisPinus armandiiPlatycladus orientalisPinus tabulaeformisPopulus davidiana + Betula albo-sinensis. The diversity and richness of shrub layer were higher than those of herb layer and arbor layer, but the evenness of arbor, shrub and herb layers had no significant difference. There were positive correlations (P0.05) between Shannon-Wiener index, Hill index, and species richness from 1 000 m to 1 920 m above sea level, but negative correlations (P0.05) from 1920 m to the top of the Mountain. The species diversity showed a "mid-altitude bulge" pattern with the change of altitude, and the reason was that the combination of temperature and moisture conditions from 1000 m to 1920 m above sea level was improved, and human disturbance was decreased gradually.