Populus euphratica and P. pruinosa are known for their high salt tolerance and the arid habitats with overlapping distributions. Here, we examined interspecific differentiation and gene flow between these two species at six loci which encoding vacuolar Na⁺/H⁺ exchanger genes. Interspecific divergence varied greatly between sampled loci and could collectively delimit the two species well. Simulations based on the isolation-migration model suggested gene flow primarily from P. euphratica into P. pruinosa. This asymmetrical gene flow may be related to the adaptive survival of the introgressed individuals. Our findings suggest that these species may have diverged in the presence of gene flow and that local adaptation may have played an important role in maintaining the distinct species lineages by restricting gene flow between them. Our results together indicate that interspecific divergence and gene flow differ greatly between members of the same gene family, possibly due to differential subfunctionalization and/or neofunctionalization during ongoing speciation of two poplar species.

Protogyny and delayed selfing are two mechanisms in facilitating outcrossing and increasing female and male function in self-compatible plant species. However, both mechanisms are rarely reported within a species. Here, we investigated pistil and stamen development, breeding system and pollination biology of the desert herb Zygophyllum macropterum by use of field observations and manipulation experiments. Our primary aim was to assess whether protogyny and delayed autonomous self-pollination occurred in this species. Zygophyllum macropterum is a spring flowering species with a floral longevity of about 3 d, including the female stage and the bisexual stage. Movement herkogamy occurred during both stages. The stigma was receptive when it was exposed from the corolla. The time of first anther dehiscence was about 12 h after stigma exposure. These results indicated that Z. macropterum is protogynous. Different pollination treatments showed that this species is self-compatible and can self-pollinate autonomously. Time of first dehiscence of anther overtopping the stigma was about 16 h after stigma exposure, suggesting that autonomous self-pollination can occur in middle-late anthesis, and thus can be defined as delayed autonomous self-pollination. Anthophora plumipes Pallas was the only pollinator of Z. macropterum. The unfavorable spring desert environment and the small corolla mouth diameter at the female stage would limit pollinator activity and thus lead to failure of outcrossing and occurrence of delayed self-pollination. Therefore, both protogyny and delayed selfing play an important role in enhancing the opportunity for outcrossing and reproductive assurance of Z. macropterum in the spring desert environment.

To better understand the elevational pattern of phylogenetic structure exhibited by alpine taxa and their underlying causes, we analyzed phylogenetic structure of each elevational belt for the alpine plants in Hengduan Mountains Region, measured by Net related index (NRI) and Net nearest taxon index (NTI). We found both the indices of phylogenetic diversity indicated that alpine plants tended to exhibit phylogenetic overdispersion at low elevational belts, implying that the distribution of alpine plants in these belts was mainly determined by interspecific competition. Alpine plants at higher elevational belts tended to phylogenetic clustering indicated by the NRI, and NTI revealed phylogenetic clustering at the belts between 4300 m and 5500 m, which presumably suggested environment filtering and rapid speciation. Above 5500 m, NTI indicated phylogenetic structure became random again, perhaps due to the low intensity of filtering and the large distances between plants at the top of the screes slopes. We concluded that phylogenetic structure was, indeed, influenced by the environmental filter, the interspecies interaction, rapid speciation during the uplift of Qinghai-Tibetan plateau and distance between plants.

Hainan, an island linking the mainland East Asia and Southeast Asia, lay in one of the ways for early migration to East Asia. The largest indigenous group of Hainan is called Hlai, which might be direct descendants of the earliest migrants. However, there are no sufficient genetic data to assess the population history of Hainan Island. Here, we have analyzed mitochondrial DNA (mtDNA) control-region and coding-region sequence variations in 566 Hlai individuals from all the five subgroups: Ha, Gei, Zwn, Moifau, and Jiamao. Our results suggest three phases for the peopling of Hainan. The first phase represents the initial settlement of the island as part of the African dispersal about 50 thousand years ago (kya). The second phase reflects colonization events from mainland Asia before the Last Glacial Maximum (LGM), which was recorded by wide distributed lineages, such as F*, B4a, and D4a.The third phase reflects population expansions under lineages F1b, M7b, and R9b after the LGM and Neolithic migrations in and out of Hainan Island. Selection also started to play a role during the last phase. We also detected different distributions between paternal Y chromosome and maternal mtDNA among isolated Hlai populations, which might be caused by sex-biased cultural practices.

Secondary cell wall, characteristic of plant cells, is a highly organized structure that provides mechanical support to the tissue and the entire plant body. Glycine soja, the presumable ancestor of domesticated soybean, differs from the domesticated soybean in an array of morphological characters. The remarkable difference is the stem phenotype, which is often attributable by the thickness of secondary cell walls. Hence, it is of great importance to understand the genetic basis underlying the regulation of secondary wall thickening. Here, we report that GlycineNST1A/B are functional orthologs of AtNST1/2, which have been shown to act as the master switches of secondary cell wall thickening. GlycineNST1A/B are preferentially expressed in organs ongoing secondary wall deposition and GmNST1A/B allele are expressed at 2-fold the level of GsNST1A/B in mature stem. The over-expression of GsNST1A/B disrupt the overall plant development by inducing ectopic deposition of massive secondary walls in normally parenchyma cells in Arabidopsis. Furthermore, expression analyses suggest that the ectopic secondary wall is achieved by up-regulating the expression of a series of cell wall associated transcription factors and secondary wall biosynthetic genes. Together, these results demonstrate that GsNST1A/B as the key regulators are capable of activating the entire secondary wall biosynthetic pathway in Arabidopsis and also suggest that the genetic circuit of secondary wall development is conserved between Fabaceae and Brassiaceae.

Geological and climatic changes in the Quaternary of the Qinghai-Tibet Plateau (Q-T Plateau) strongly affect the migration route and distribution pattern of the plants in this region. The Angelica nitida Wolff endemic to the Q-T Plateau was used as a model to examine the response to Quaternary climatic oscillations. Three chloroplast DNA fragments (trnD-trnT, trnQ-rps16, rpl32-trnL) were sequenced and 20 haplotypes were identified. The 20 haplotypes clustered into 4 major clades, which were associated with geographical distribution, and the populations from the edge of Q-T Plateau contained 19 haplotypes. Based on the average substitution rate, the divergence time in A. nitida was estimated at 1.1 million years ago (Mya), 0.80 Mya and 0.70 Mya, corresponding to the recently continuous uplift of the Q-T Plateau and the interglacial in the Quaternary. A significant phylogeographic structure was presented (N_ST> G_ST, P < 0.01). Our results also suggested that multiple refugia for A. nitida were located on the edge of the Q-T Plateau in the Quaternary. The restricted gene flow and past fragmentation were likely the major processes that shaped the present-day spatial distribution of haplotypes in this species. These results suggested that past fragmentation mainly resulted from the maximum glaciation advance on Q-T Plateau. The uplift of Loess Plateau, Huya fault of Minshan Mountain could also played important roles responsible for the present phylogeographical pattern of A. nitida.

Nymphoides peltata is a distylous aquatic plant. In order to explore the relative importance of clonal growth and sexual reproduction within populations and also to reveal the origin of the commonly occurred one style morph populations in China, we studied the clonal diversity and population genetic structure of this species. By using seven SSR primer pairs, a total of 192 multilocus genotypes (MLGs) were identified among the 472 samples from the 21 populations analyzed and each population has two or more MLGs. The number of MLGs was lower for the one style morph populations than distylous populations. Analysis of Molecular Variance (AMOVA) showed that a smaller proportion of genetic variation resided among populations (36.8%). Neighbor-joining (NJ) tree indicated that there was no significant geographical structure of the genetic variation among populations of Nymphoides peltata. The BOTTLENECK tests indicated that there had been significant bottlenecks in most of the studied populations. The successful sexual recruitment from seeds may have contributed to the high clonal diversity in distylous populations of N. peltata in China. Demographic stochasticity or bottleneck should account for the one style morph population with several MLGs. And also the bottleneck effects or demographic changes caused by human activities occurred randomly in populations should account for the finding of no significant geographical structure of the genetic variation among the investigated populations of N. peltata.

As the most abundant protein in the earth, RuBisCO is the key enzyme in carbon fixation of photosynthesis in all green plants. RuBisCO is hexadecimal polymer, consisting of two kinds of subunits, large and small ones, which are encoded by different genomes. The large subunit is encoded by chloroplast genome while small one by nuclear genome. The function of RuBisCO relies on the two subunits, and only when they are combined to be hexadecimal, can it perform the whole function. However, how the large and small subunits evolved, if ever coevolved, has remained mysterious. In this study, based on data in 21 species, phylogenies were analyzed on two subunits respectively, and a mirror tree was reconstructed to reveal phylogenetic similarity. Furthermore, a comparative analysis method, using the codon usage bias and correlation calculation for RuBisCO subunits, was performed. The RSCU (Relative Synonymous Codon Usage) values of large and small subunits were calculated respectively. Finally, a novel parameter, RDC (RSCU Distances-based Correlation), for evaluating molecular coevolution was proposed based on Pearson correlation coefficient between RSCU value matrices of two subunits. The results show that the topological similarity of mirror tree gave positive evidence of coevolution between subunits. Similarly, the RDC was high, 0.558, revealing that the RuBisCO subunits coevolved to an extent. The present results confirmed that coevolution happened between the two subunits of RuBisCO, although they were encoded by different genomes. This study added new evidence that function constrain plays even more important role in evolution of the two subunits.

Nymphoides peltata is a distylous aquatic plant. In order to explore the relative importance of clonal growth and sexual reproduction within populations and also to reveal the origin of the commonly occurred one style morph populations in China, we studied the clonal diversity and population genetic structure of this species. By using seven SSR primer pairs, a total of 192 multilocus genotypes (MLGs) were identified among the 472 samples from the 21 populations analyzed and each population has two or more MLGs. The number of MLGs was lower for the one style morph populations than distylous populations. Analysis of Molecular Variance (AMOVA) showed that a smaller proportion of genetic variation resided among populations (36.8%). Neighbor-joining (NJ) tree indicated that there was no significant geographical structure of the genetic variation among populations of Nymphoides peltata. The BOTTLENECK tests indicated that there had been significant bottlenecks in most of the studied populations. The successful sexual recruitment from seeds may have contributed to the high clonal diversity in distylous populations of N. peltata in China. Demographic stochasticity or bottleneck should account for the one style morph population with several MLGs. And also the bottleneck effects or demographic changes caused by human activities occurred randomly in populations should account for the finding of no significant geographical structure of the genetic variation among the investigated populations of N. peltata.

As the most abundant protein in the earth, RuBisCO is the key enzyme in carbon fixation of photosynthesis in all green plants. RuBisCO is hexadecimal polymer, consisting of two kinds of subunits, large and small ones, which are encoded by different genomes. The large subunit is encoded by chloroplast genome while small one by nuclear genome. The function of RuBisCO relies on the two subunits, and only when they are combined to be hexadecimal, can it perform the whole function. However, how the large and small subunits evolved, if ever coevolved, has remained mysterious. In this study, based on data in 21 species, phylogenies were analyzed on two subunits respectively, and a mirror tree was reconstructed to reveal phylogenetic similarity. Furthermore, a comparative analysis method, using the codon usage bias and correlation calculation for RuBisCO subunits, was performed. The RSCU (Relative Synonymous Codon Usage) values of large and small subunits were calculated respectively. Finally, a novel parameter, RDC (RSCU Distances-based Correlation), for evaluating molecular coevolution was proposed based on Pearson correlation coefficient between RSCU value matrices of two subunits. The results show that the topological similarity of mirror tree gave positive evidence of coevolution between subunits. Similarly, the RDC was high, 0.558, revealing that the RuBisCO subunits coevolved to an extent. The present results confirmed that coevolution happened between the two subunits of RuBisCO, although they were encoded by different genomes. This study added new evidence that function constrain plays even more important role in evolution of the two subunits.

Pedicularis exhibits high diversity in its corolla form. However, floral ontogeny has been rarely investigated. Particularly, the development of the highly variable upper lip (galea), three broad morphological types of which (beakless and toothless; beakless and toothed; beaked) can be discriminated, remains unknown. We used scanning electron microscopy (SEM) to investigate the early stages of floral ontogeny in two beaked species, Pedicularis gruina and P. siphonantha. To compare developmental process of the three galea types, three species for each type were investigated. Initiations of floral organs in Pedicularis are consistent. Sepal initiations are successive from the lateral-adaxial primordia, followed by the lateral-abaxial ones (these sometimes missing), then the mid-adaxial one (again sometimes missing). The stamens are initiated prior to the petals, or development of petal primordia may be retarded at the early stages in comparison with that of stamen primordia. Four stamen primordia are initiated simultaneously. The five petal primordia are initiated almost simultaneously. Development processes of the upper lip among the three galea types differ in the expansion rates and directions of the cells of the two lobes and these differences govern whether or not a beak and/or teeth are formed on the upper lip. The floral ontogeny of Pedicularis is close to that of Agalinis, which supports the molecular assignment. Floral monosymmetry of Pedicularis is established at the beginning of sepal initiation and is maintained until flowering. The development of the upper lip provides some clues to the evolution of beaked and/or toothed galeas in Pedicularis.

The species delimitation of Lemmaphyllum, including the former segregated Lepidogrammitis in China, was considered as unresolved. Previous treatments accepted one or up to 20 species. In the present study, a multivariate analysis and maximum parsimony analyses were performed on data from herbarium specimens of this genus by evaluating 24 quantitative characters and 13 qualitative characters. In total, 558 specimens representing 11 previously accepted species and one variety in China were studied. As a result, three species and two varieties were recognized: Lemmaphyllum pyriforme, L. rostratum, L. carnosum, L. carnosum var. microphyllum and L. carnosum var. drymoglossoides. Two new combinations and seven new synonyms were introduced. An identification key and distribution maps were provided. This study also elucidated the diagnostic value of two previously ignored characters: scales at the base of stipe and laminae hydathodes.

Nuclear ribosomal ITS and four cpDNA intergenic spacer sequences were used to assess how the patterns of molecular differentiation are related to taxonomic boundaries and geographic distribution in polymorphic and taxonomically complex Orostachys subsection Orostachys (Crassulaceae). Two major cpDNA lineages were identified in a set of Orostachys populations, lineage A, comprising 13 closely related haplotypes found in 11 populations of monocarpic O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii and lineage B that included 9 out of 10 divergent haplotypes found in five populations of O. paradoxa, distinct in perennial stoloniferous habit. Our data suggest that the current concepts of O. malacophylla var. malacophylla, O. maximowiczii and O. gorovoii are incompatible with the differentiation at the cpDNA level. Neither of these taxa could be allied to a particular haplotype or haplotype clade. The pattern of relationships between 7 ITS ribotypes found in 17 populations supported neither the morphology-based taxonomic subdivision in the subsection Orostachys nor grouping according to geographical origin of the populations or lineages recovered with cpDNA data. A high level of similarity of ITS rDNA sequences between the subsection members suggests their relatively recent and rapid divergence from a common ancestor.

Despite several morphological and molecular analyses of Theaceae, several outstanding issues remain in the phylogenetics and biogeography of the family including the disputed relationships among the tribes Gordonieae, Stewartieae, and Theeae, the controversial taxonomic status of Hartia and Stewartia, and the unclear biogeographic history of Gordonieae and Stewartieae. In this study we gathered DNA sequences of multiple plastid genes from 27 species of Theaceae representing all genera except Laplacea, conducted phylogenetic analyses using parsimony, likelihood, and Bayesian methods, and estimated divergence times within a Bayesian framework with fossil calibrations and molecular data. Our data provided further support for the three tribes in the family and for the sister-group relationship of Theeae to Stewartieae plus Gordonieae. Within Gordonieae, our study for the first time offered strong molecular support for the sister relationship of Franklinia and Schima. Within Stewartieae, our data supported the paraphyly of Stewartia including Hartia. Within Stewartia, our data for the first time suggested that North American (NA) species S. ovata was more closely related to eastern Asian (EA) species than to the other NA species S. malacodendron. Biogeographic analyses indicated that disjunct endemic species of Gordonieae might have originated from NA and those of Stewartieae from EA. Divergence times of the EA-NA disjunct pairs identified in this study (Franklinia and Schima in Gordonieae and Stewartia ovata (NA) and Asian species of Stewartia) were estimated to be in the Mid-Miocene. Population exchanges in Gordonieae and Stewartieae may have occurred over the Bering land bridge prior to the Mid-Miocene.

This paper deals with species of the genus Cyclosorus subgenus Cyclosoriopsis (Thelypteridaceae) from China, which is characterized by goniopteroid venation and unicellular glands on sporangial stalks. Morphological study of specimens and living plants reveals that venation and glands/glandular hairs on laminae are the most important diagnostic characters for species identification. Twenty-two species are recognized, including seven species endemic to China. Fifty species names are newly reduced to synonyms. A key to species from China, description and distribution map of each species are provided. Three species are treated as dubious species, and twenty-two species are treated as putative hybrids.

To investigate the genetic differences in Chinese large-flowered chrysanthemum (Chrysanthemum × morifolium Ramat.) cultivars, we selected 40 typical and stable cultivars on which to carry out cytological studies using karyotype analysis. The results showed that 67.5% of these cultivars were hexaploid-based aneuploid and that the proportion of hexaploid decreased with passing time. Moreover, 35% of the cultivars had 1–4 satellite chromosome(s). The probability of satellite chromosomes rose with increasing chromosome number. Most of the karyotypes were 2A and 2B. The probability of types 2A and 2C also increased with increasing ploidy of the cultivars. The mean of long-/short-arm ratio and the variation of long-/short-arm ratio were positively correlated (r² = 0.72). There was no obvious difference in the asymmetry coefficient of karyotypes, but the discrepancy in the variance of karyotype asymmetry index and relative length of chromosomes was quite distinct. In terms of karyotype parameters, the petal types of chrysanthemums were classified to five groups as flat, tubular, spoon, abnormal, and anemone. We did not observe any obvious orderliness among flower head types. Considering the relationship between karyotype parameters and phenotypic characters, variation of long-/short-arm ratio and asymmetry coefficient of karyotypes had the greatest relevance toward most phenotypic characters. The above results indicate that karyotype parameters possess great values for cultivar identification, classification, and genetic analysis in chrysanthemums.

Nuclear ribosomal ITS and four cpDNA intergenic spacer sequences were used to assess how the patterns of molecular differentiation are related to taxonomic boundaries and geographic distribution in polymorphic and taxonomically complex Orostachys subsection Orostachys (Crassulaceae). Two major cpDNA lineages were identified in a set of Orostachys populations, lineage A, comprising 13 closely related haplotypes found in 11 populations of monocarpic O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii and lineage B that included 9 out of 10 divergent haplotypes found in five populations of O. paradoxa, distinct in perennial stoloniferous habit. Our data suggest that the current concepts of O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii are incompatible with the differentiation at the cpDNA level. Neither of these taxa could be allied to a particular haplotype or haplotype clade. The pattern of relationships between 7 ITS ribotypes found in 17 populations supported neither the morphology-based taxonomic subdivision in the subsection Orostachys nor grouping according to geographical origin of the populations or lineages recovered with cpDNA data. A high level of similarity of ITS rDNA sequences between the subsection members suggests their relatively recent and rapid divergence from a common ancestor.

Despite several morphological and molecular analyses of Theaceae, several outstanding issues remain in the phylogenetics and biogeography of the family including the disputed relationships among the tribes Gordonieae, Stewartieae, and Theeae, the controversial taxonomic status of Hartia and Stewartia, and the unclear biogeographic history of Gordonieae and Stewartieae. In this study we gathered DNA sequences of multiple plastid genes from 27 species of Theaceae representing all genera except Laplacea, conducted phylogenetic analyses using parsimony, likelihood, and Bayesian methods, and estimated divergence times within a Bayesian framework with fossil calibrations and molecular data. Our data provided further support for the three tribes in the family and for the sister-group relationship of Theeae to Stewartieae plus Gordonieae. Within Gordonieae, our study for the first time offered strong molecular support for the sister relationship of Franklinia and Schima. Within Stewartieae, our data supported the paraphyly of Stewartia including Hartia. Within Stewartia, our data for the first time suggested that North American (NA) species Stewartia ovata was more closely related to eastern Asian (EA) species than to the other NA species Stewartia malacodendron. Biogeographic analyses indicated that disjunct endemic species of Gordonieae might have originated from NA and those of Stewartieae from EA. Divergence times of the EA-NA disjunct pairs identified in this study (Franklinia and Schima in Gordonieae and S. ovata (NA) and Asian species of Stewartia) were estimated to be in the Mid-Miocene. Population exchanges in Gordonieae and Stewartieae may have occurred over the Bering land bridge prior to the Mid-Miocene.

Orchids are known for their beauty and complexity of flower and ecological strategies. The evolution in orchid floral morphology, structure, and physiological properties has held the fascination of botanists for centuries, from Darwin through to the present. In floral studies, MADS-box genes contributing to the now famous ABCDE model of floral organ identity control have dominated conceptual thinking. The sophisticated orchid floral organization offers an opportunity to discover new variant genes and different levels of complexity to the ABCDE model. Recently, several remarkable research reports on orchid MADS-box genes, especially B-class MADS-box genes, have revealed the evolutionary track and important functions on orchid floral development. Diversification and fixation of both paleoAP3 gene sequences and expression profiles might be explained by subfunctionalization and even neofunctionalization. Knowledge about MADS-box genes encoding ABCDE functions in orchids will give insights into the highly evolved floral morphogenetic networks of orchids.

Soil hosts diverse communities of photosynthetic eukaryotes (algae) that have not yet been fully explored. Here we describe an interesting coccoid green alga isolated from a soil sample from a forest-steppe in South Urals (Bashkortostan, Russia) that, based on a phylogenetic analysis of 18S rRNA gene sequence, appears to represent a new phylogenetic lineage related to the genus Leptosira within the class Trebouxiophyceae. This new alga is characterized by uninucleate cells with a shape ranging from spherical to ellipsoid or egg-like, occurring solitary or more often grouped in irregular masses or colonies. Remarkably, cells with a characteristic pyriform shape are encountered in cultures grown on a solid medium. The cells harbour a single pyrenoid-lacking parietal chloroplast with the margin undulated or forming finger-like projections; in mature cells the chloroplast becomes divided by deep incisions into more or less separate lobes. Transmission electron microscopy of vegetative cells revealed an unprecedented structure in the form of a cluster of microfibrils located in the cytoplasm near the plasma membrane, often appressed to the chloroplast. Reproduction takes place via autospores or biflagellated zoospores. The unique suite of characters of our isolate distinguishes it from previously described coccoid green algae and suggests that it should be classified as a new species in a new genus; we propose it be named Chloropyrula uraliensis.

To obtain a better understanding of how Quaternary climatic oscillations influenced range distributions and intraspecific split of alpine plants on the Qinghai–Tibetan Plateau (QTP) and in adjacent regions, we investigated the extant phylogeographical structure of Bupleurum smithii in this area based on 22 populations and 103 individuals spanning the entire distribution region of this species using chloroplast DNA sequences. Two major haplotype lineages were identified, and at least two corresponding glacial refugia maintaining in the northeastern and eastern edge of the QTP during the Last Glacial Maximum were revealed. Secondary contact between populations and efficient gene flow were also found between two major haplotype lineages. In addition, based on the geographic distribution of haplotypes, we found that populations on the platform derived from individuals that recolonized this area from refugia situated at the northeastern and eastern edges of the QTP, and that B. smithii recolonized from southern to northern China during inter- and post-glacial periods.

A previous study with amplified fragment length polymorphism (AFLP) fingerprints found no evidence of genetic impoverishment in the endangered Centaurea borjae and recommended that four management units (MUs) should be designated. Nevertheless, the high ploidy (6x) of this narrow endemic plant suggested that these conclusions should be validated by independent evidence derived from non-nuclear markers. Here, the variable trnT-F region of the plastid genome was sequenced to obtain this new evidence and to provide an historical background for the current genetic structure. Plastid sequences revealed little genetic variation; calling into question the previous conclusion that C. borjae does not undergo genetic impoverishment. By contrast, the conclusion that gene flow must be low was reinforced by the strong genetic differentiation detected among populations using plastid sequences (global F_ST = 0.419). The spatial arrangement of haplotypes and diversity indicate that the populations currently located at the center of the species range are probable sites of long-persistence whereas the remaining sites may have derived from a latter colonization. From a conservation perspective, four populations contributed most to the allelic richness of the plastid genome of the species and should be given priority. Combined with previous AFLP results, these new data recommended that five, instead of four, MUs should be established. Altogether, our study highlights the benefits of combining markers with different modes of inheritance to design accurate conservation guidelines and to obtain clues on the evolutionary processes behind the present-day genetic structures.

Palynological analysis of 24 samples from four types of natural pollen traps (Lugu Lake bottom sediments, surface soil, bark samples, and moss cushions) in four sites at different altitudes from the Lugu Lake area, southwest China, has been undertaken to investigate pollen dispersal and deposition in a mountainous area and assist with the interpretation of fossil pollen analysis. Detailed comparisons between the palynological assemblage and the modern vegetation in the Lugu Lake region have been carried out. Preliminary interpretations of the correlation between pollen assemblage and vegetation at the different vertical vegetational zones can be recognized by the percentages of the main taxa, and most of the pollen taxa except Pinus are expected to be underrepresented. Exotic pollen grains can be transported over mountains more than 70 km away by wind. Upslope or downslope transport of pollen grains is crucial when reconstructing palaeoclimate in mountainous areas. We summarize the altitudinal distributions of modern woody plants whose pollen grains are present at three sites, and reveal that pollen grains are more readily carried uphill than downhill. These findings have important implications regarding the reconstruction of vegetation in mountainous regions and the interpretion of palaeoelevations.

Rhododendron ×duclouxii is morphologically intermediate between Rhododendron spiciferum and Rhododendron spinuliferum, and was suspected to be a natural hybrid between these species. In this study, the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F regions of 34 accessions of R. ×duclouxii and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology demonstrated that R. ×duclouxii represents a natural hybrid between R. spiciferum and R. spinuliferum. It also implies that the hybridization between R. spiciferum and R. spinuliferum is bidirectional, and that populations of R. ×duclouxii represent hybrid swarms from backcrossing or selfing of F₁ plants. The study is important for understanding the speciation processes in the genus since it demonstrates for the first time the existence of a natural homoploid hybrid in Rhododendron subgenus Rhododendron.

Flower orientation has been considered one aspect of floral attraction. Plants growing on slopes should orientate their flowers facing down slope towards greater open space to enhance reproduction by attracting more pollinators. Flower angle and floral symmetry may affect this pattern; for example, this trend would be overshadowed in vertical/pendent flowers with radial symmetry because the flowers can attract pollinators and provide landing platforms from many directions. We investigated this hypothesis in Lilium duchartrei, a herb with pendent and actinomorphic flowers, in the Hengduan Mountains region of China by measuring flower direction for individuals growing on flat ground and on slopes. We also changed flower direction from facing down to up slope to test the effects on pollinator visitation frequency and subsequent plant reproduction. Plants growing on flat ground orientate their flowers equally towards the four geomagnetic directions, whereas the flowers on individuals growing on slopes preferentially face down slope. This pattern was more pronounced for individuals growing on steeper slopes. There was a positive correlation between slope angle and the seed set of flowers facing down slope (control), but a negative correlation between seed set and flowers facing up slope. The visitation frequency also tended to be higher for control flowers on steeper slopes and lower for those flowers changed to face up slope. Unexpectedly, floral direction was not affected by flower angle or floral symmetry. The results suggest that a down slope orientation of flowers could function to improve pollination in heterogeneous pollination environments.

Resource allocation, as well as the tradeoffs among different reproductive components, plays an important role in the adaptability of plants to different environments. The hybrid may exhibit a higher adaptability in life history in heterogeneous environments because of the genetic variation derived from its parents. In this study, we exploited three levels of water depths and two types of sediments to investigate the resource allocation pattern of the first generation of the natural hybrid Potamogeton ×intortifolius compared to its parents P. wrightii and P. perfoliatus. We also measured the ramet survivorship and the seed set of the hybrid P. ×intortifolius. Our results showed that P. ×intortifolius had higher ramet survival than its parents at 1.5-m water depth on clay sediment. The possible tradeoffs showed that in P. ×intortifolius the tradeoff pattern between sexual and clonal reproduction was more pronounced in limiting environments. The individuals allocated more resources to sexual reproduction when the environment was limiting, which might confer a higher ability to utilize resources, to produce offspring and to found new populations. Although the seed set of P. ×intortifolius was lower than its parents, it had a higher ability to increase its seed set when the environment was limiting (sandy sediment) than its parents, which might benefit its future survival. These results indicated that the F₁ hybrid P. ×intortifolius was more able to adapt to limiting environments than one or both of its two parental taxa.

The Qinghai–Tibetan Plateau (QTP), known as “the Roof of the World”, is one of the most unique and vulnerable biodiversity regions on Earth. However, the spatial patterns and determinants of vascular plant diversity on the QTP are still poorly documented, despite a number of publications focusing on its flora. Using extensively compiled data gathered from local flora and specimen records, we evaluated the relative importance of water, energy, and habitat heterogeneity-related variables in shaping the distribution of vascular plant diversity (species, genus, family, herb, woody plants). We found that higher richness always occurred in the south and east of the QTP, especially along the Himalayas, and that habitat heterogeneity, water, and energy variables are important determinants of vascular plant richness patterns on the QTP. The explanatory power of most single predictors was obviously different across life forms, with woody plant richness generally more sensitive to most environmental factors than herb richness. In addition, the explanatory power of habitat heterogeneity models, combined water and energy models, and environmental models increased as the taxonomic level increased from species to family. The results highlight that correlations between plant richness and environmental variables vary with life form and taxonomic scale, and suggest that the explanatory power of variables will change in different spatial scales due to the proportion of life forms and the asymmetric effects of these drivers on life form richness.

The systematic position of the small neotropical genus Oryzolejeunea (three spp.) has long been controversial. Phylogenetic analyses of molecular data for the present study using DNA markers (trnL, psbA, and a nuclear ribosomal internal transcribed spacer [nrITS] region) shows that the genus is nested in Lejeunea. The results not only reveal the phylogenetic position of Oryzolejeunea for the first time, but also challenge the taxonomic value of the proximal hyaline papilla as a key feature in Lejeunea. The present study shows the urgent need for a reassessment of the perimeters of the genus Lejeunea and its infrageneric classification. Three new combinations, namely Lejeunea saccatiloba, Lejeunea grolleana, and Lejeunea venezuelana, are proposed.

Effective conservation of crop wild relative (CWR) species is essential for the sustainable use and genetic improvement of crop varieties, which offers greater opportunities for world food security, particularly in modern agroecosystems where CWR diversity is under severe threat. Factors such as habitat fragmentation, human disturbances, global climate change, and invasion of harmful alien species have been identified to be responsible for losses and threats to CWR diversity. However, a neglected factor, gene introgression from domesticated species through repeated outcrossing, may have a significant impact on CWR diversity. Introgression can influence genetic diversity and evolutionary processes of CWR populations through effects such as demographic swarming, genetic assimilation, and selective sweep. When largely enhancing or reducing fitness of wild plants, the introgression of crop genes will impose more significant genetic and evolutionary impacts on CWR populations, leading to undesired consequences for conserved CWR populations and species. This situation is particularly true when genetically engineered (GE) crops are deployed for commercial cultivation. It is argued that a GE crop usually contains transgenes with strong natural selection advantages, and such transgenes introgressed into CWR populations may have strong impacts on their genetic diversity and evolutionary processes, threatening their conservation. This article reviews the challenge of crop–wild gene flow, and particularly transgene introgression from GE crops, for the in situ conservation of wild relative species. The design of effective management strategies for conserving CWR species under the scenario of extensive cultivation of GE crops is also discussed.

The origins of Kam-Sui speaking Chadong and Mulam people have been controversial subjects in ethnic history studies and other related fields. Here, we studied Y chromosome (40 informative single nucleotide polymorphisms and 17 short tandem repeats in a non-recombining region) and mtDNA (hypervariable segment I and coding region single nucleotide polymorphisms) diversities in 50 Chadong and 93 Mulam individuals. The Y chromosome and mtDNA haplogroup components and network analyses indicated that both Chadong and Mulam originated from the admixture between surrounding populations and the indigenous Kam-Sui populations. The newly found Chadong is more closely related to Mulam than to Maonan, especially in the maternal lineages.

Linguistics and genetics always reach similar results in phylogenetic studies of human populations. A previous study found that populations speaking Han Chinese dialects have closer genetic relationships to each other than to neighboring ethnic groups. However, the Pinghua Chinese population from Guangxi is an exception. We have reported that northern Pinghua people are genetically related to populations speaking Daic languages. In this study, we further studied the southern Pinghua population. The Y chromosome and mitochondrial DNA haplogroup components and network analysis indicated that northern and southern Pinghua populations were genetically different. Therefore, we concluded that the Pinghua speakers may have various origins, even though Pinghua dialects are similar. Pinghua dialects might have originated when the Daic or Hmongic speakers from different regions learnt to speak the same Chinese dialect hundreds of years ago. Speakers of one language do not always have just one origin.

Y chromosome haplogroup O3-M122 is the most prevalent haplogroup in East Asia, and provides an ideal tool for dissecting primary dispersals of the East Asians. Most of the sub-haplogroups of O3-M122 have been sufficiently investigated except for O3a1c-002611, despite its great prevalence and huge population, especially in Han Chinese. In this study, we identified 508 individuals with haplogroup O3a1c-002611 out of 7801 males from 117 East and Southeast Asian populations, typed at two newly discovered downstream Y-SNP markers and ten commonly used Y-STRs. Defined by SNPs IMS-JST002611 (in short, 002611), F11, and F238, three lineages internal to haplogroup O3a1c-002611 have distinct geographical distributions. Furthermore, Y-STR diversity shows a general south-to-north decline, which is consistent with the prehistorically northward migration of the other O3-M122 lineages. The northward migration of haplogroup O3a1c-002611 started about 13 thousand years ago (KYA). The expansions of subclades F11 and F238 in ancient Han Chinese began about 5 and 7 KYA immediately after the separation between the ancestors of the Han Chinese and Tibeto-Burman.

The Utsat people do not belong to one of the recognized ethnic groups in Hainan, China. Some historical literature and linguistic classification confirm a close cultural relationship between the Utsat and Cham people; however, the genetic relationship between these two populations is not known. In the present study, we typed paternal Y chromosome and maternal mitochondrial (mt) DNA markers in 102 Utsat people to gain a better understanding of the genetic history of this population. High frequencies of the Y chromosome haplogroup O1a*-M119 and mtDNA lineages D4, F2a, F1b, F1a1, B5a, M8a, M*, D5, and B4a exhibit a pattern similar to that seen in neighboring indigenous populations. Cluster analyses (principal component analyses and networks) of the Utsat, Cham, and other ethnic groups in East Asia indicate that the Utsat are much closer to the Hainan indigenous ethnic groups than to the Cham and other mainland southeast Asian populations. These findings suggest that the origins of the Utsat likely involved massive assimilation of indigenous ethnic groups. During the assimilation process, the language of Utsat has been structurally changed to a tonal language; however, their Islamic beliefs may have helped to keep their culture and self-identification.

The history of some invasive species is so complex that their origins can be difficult to determine. One example of such invasive species is the California invasive known as “wild artichoke thistle” (Cynara cardunculus var. sylvestris), found in natural and disturbed ecosystems. Wild artichoke thistle is a Mediterranean native and the progenitor of two domesticated horticultural taxa, artichoke and cardoon. Different hypotheses regarding the origins of California plants have included introductions by 19th century Italian immigrants and the de-domestication (evolutionary reversion to wild-type morphology) of feral (escaped, free-living) cultivars. Using microsatellite markers, we compared the genetic constitutions of 12 artichoke thistle populations in California with possible progenitor populations: 17 Spanish and Italian wild populations and eight different artichoke and cardoon cultivars. Each California population was compared with its putative progenitors using STRUCTURE analysis. Our results suggest that California's artichoke thistle populations are polyphyletic. Surprisingly, two-thirds of California's populations closely matched populations from the Iberian Peninsula. Three populations matched domesticated artichoke. One population appears to have wild and cultivar hybrid ancestry. Alleles specific to Italian populations were found at low frequencies in some California plants, suggesting that Italian wild plants may have been in California, but have left a trivial genetic legacy. Given that the de-domesticated plants in this study appear to be as invasive as the wild taxon, we conclude with a discussion of the role that ferality and de-domestication may have in plant invasions.

Interactions between herbivore pressure and resource availability may result in growth–defense trade-offs in plants (resource availability hypothesis), which promote the potential for ecological diversification and have recently been proposed as a new mechanism of plant invasion (resource–enemy release hypothesis). In the present study, we tested this idea by comparing patterns of maximum growth rate and antiherbivore defense capacity against Agasicles hygrophila (a specialist phytophagous insect on Alternanthera philoxeroides) among six morphs of A. philoxeroides from both native (Argentina) and introduced (US and China) ranges. The results revealed that herbivore resistance consistently exhibited a significant trade-off against the growth rate of A. philoxeroides. Compared with native morphs in Argentina, introduced morphs generally exhibited a higher growth rate and lower defense. The results demonstrate that the combination of flea beetle pressure and resource availability facilitates geographical divergence of A. philoxeroides, and that release from natural specialists and increased resource availability may interact to contribute to its successful invasion.

Plant responses to crowding have been investigated extensively in stands of light-demanding species, but shade-tolerant species may react differently. In the present study, we investigated the effect of density on the mortality, size inequality, and biomass allocation of Alternanthera philoxeroides, a shade-tolerant invasive species. Stem fragments of A. philoxeroides were grown at either low or high densities (6 vs. 24 plants per pot) under three light levels (10%, 34%, and 100% full sun). After 8 weeks, survival was 31% lower in pots with a higher initial density. Both high density and low light levels reduced plant size substantially. Mean plant biomass ranged from 0.23 g in high-density and low-light pots to 4.41 g in low-density and high-light pots. There were no strong or significant effects of density or light level on size inequality of survivors. Most of the variation in allocation and morphology in response to light level and crowding were due to plant size and allometric growth, with little evidence of true plasticity. There was a small but significant increase in shoot allocation, in the direction predicted by optimal allocation theory, at low light levels. Our results show that intense competition need not be size asymmetric, and suggest that tolerance to low light levels involves a reduction in phenotypic plasticity. Responses of the invasive A. philoxeroides to crowding may be an example of an invasive plant's success in establishing dense stands of closely related individuals that are shade tolerant, cooperative, and follow a relatively fixed allometric trajectory with low plasticity.

The genus Cucurbita (Cucurbitaceae) includes five species that were domesticated independently in the Americas, giving rise to an immense diversity of squashes, pumpkins, and gourds. To gain an improved understanding of the evolution of Cucurbita and its domesticated taxa, we used four chloroplast loci to estimate the phylogeny of 23 taxa that represent the broad-level diversity within Cucurbita. Our results provide a strongly supported framework hypothesis for the phylogeny of the genus, robustly confirming the basal position of the C. digitata group of xerophytic perennials and the monophyly of a large group of mesophytic annuals that represent most of the known diversity in the genus, both wild and domesticated. The chloroplast evidence provides strong support for a novel grouping of the mesophytic annual C. ficifolia (known only from cultivation) with the xerophytic perennials C. foetidissima and C. pedatifolia. This study also provides the first DNA-based evidence in support of the isozyme-based hypothesis that C. pepo subsp. ovifera var. ovifera (represented by most ornamental gourds and several squashes) was domesticated from the wild taxon C. pepo subsp. ovifera var. ozarkana. This lends support to the hypothesis that var. ovifera was domesticated in the eastern United States and that this region served as one of about 10 independent centers of origin of human agriculture. Although the level of bootstrap support for this and certain other peripheral relationships in Cucurbita is low, definitive resolution of these issues is within reach, as next-generation sequencing should soon deliver entire organelle genome sequences from a comprehensive sampling of the genus.

To investigate the genetic differences in Chinese large-flowered chrysanthemum (Chrysanthemum×morifolium Ramat.) cultivars, we selected 40 typical and stable cultivars on which to carry out cytological studies using karyotype analysis. The results showed that 67.5% of these cultivars were hexaploid-based aneuploid and that the proportion of hexaploid decreased with passing time. Moreover, 35% of the cultivars had 1–4 satellite chromosome(s). The probability of satellite chromosomes rose with increasing chromosome number. Most of the karyotypes were 2A and 2B. The probability of types 2A and 2C also increased with increasing ploidy of the cultivars. The mean of long-/short-arm ratio and the variation of long-/short-arm ratio were positively correlated (r² = 0.72). There was no obvious difference in the asymmetry coefficient of karyotypes, but the discrepancy in the variance of karyotype asymmetry index and relative length of chromosomes was quite distinct. In terms of karyotype parameters, the petal types of chrysanthemums were classified to five groups as flat, tubular, spoon, abnormal, and anemone. We did not observe any obvious orderliness among flower head types. Considering the relationship between karyotype parameters and phenotypic characters, variation of long-/short-arm ratio and asymmetry coefficient of karyotypes had the greatest relevance toward most phenotypic characters. The above results indicate that karyotype parameters possess great values for cultivar identification, classification, and genetic analysis in chrysanthemums.

Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which plays a key role in the transmission of human blood fluke Schistosoma. The complete mitochondrial (mt) genome of O. hupensis has been characterized; however, the phylogenetic performance of mt protein-coding genes (PCGs) of the snail remain unclear. In this study, 11 whole mt genomes of snails collected from four different ecological settings in China and the Philippines were sequenced. The mt genome sizes ranged from 15 183 to 15 216 bp, with the G + C contents from 32.4% to 33.4%. A total of 15 251 characters were generated from the multiple sequence alignment. Of 2711 (17.8%) polymorphic sites, 56.22% (1524) were parsimony sites. The mt genomes' phylogenetic trees were reconstructed using minimum evolution, neighbor joining, maximum likelihood, maximum parsimony, and Bayesian tree estimate methods, and two main distinct clades were identified: (i) the isolate from mountainous regions; (ii) the remaining isolate which included three inner branches. All phylogenetic trees of the 13 PCGs were generated by running 1000 bootstrap replicates and compared with the complete mtDNA tree, the classification accuracy ranging from 21.23% to 87.87%, the topological distance of phylogenetic trees between PCGs ranging from 5 to 14. Therefore, the performance of PCGs can be divided into good condition (COI, ND2, ND5, and ND3), medium (COII, ATP6, ND1, ND6, Cytb, ND4, and COIII), poor (ATP8 and ND4L). This study represents the first analysis of mt genome diversity of the O. hupensis snail and phylogenetic performance of mt PCGs. It presents clear evidence that the snail populations can be separated into four landscape genetic populations in mainland China based on whole mt genomes. The identification of the phylogenetic performance of PCGs provides new insight into the intensive genetic diversity study using mtDNA markers for the snail.

Recently, several statistical methods have been independently proposed for estimating the degree (n) of gene pleiotropy (i.e. the capacity of a gene to affect many phenotypes) without knowing measurable phenotypic traits. However, the theoretical limitation of these approaches has not been well demonstrated. In this short note, we show that our previous method based on the phylogeny of protein sequences is, in fact, an effective estimate of a parameter that can be written symbolically as K = min(n,r), where r is the rank of mutations at an amino acid site. Hence, understanding of r is crucial for appropriate interpretation of the estimated K, denoted by K_e (the effective gene pleiotropy). Indeed, when protein sequence alignment is used to estimate effective gene pleiotropy (K_e) by this method, K_e can be interpreted as an effective estimate of n when n ≤ 20, as long as the phylogeny is sufficiently large. If n > 20, K_e → 20, although the true n could be much higher.