Geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in ChinaOA

China covers a vast territory harbouring a large number of aquatic plants.Although there are many studies on the β-diversity of total,herbaceous or woody plants in China and elsewhere,few studies have focused on aquatic plants.Here,we analyse a comprehensive data set of 889 aquatic angiosperm species in China,and explore the geographic patterns and climatic correlates of total taxonomic and phylogeneticβ-diversity as well as their turnover and nestedness components.Our results show that geograph...     

Global patterns of taxonomic and phylogenetic diversity of flowering plants:Biodiversity hotspots and coldspotsOA

Species diversity of angiosperms(flowering plants) varies greatly among regions.Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes.Here,using a comprehensive data set for regional angiosperm floras across the world,we show geographic patterns of taxonomic(species) diversity,phylogenetic diversity,phylogenetic dispersion,and phylogenetic deviation(i.e.,phylogenetic diversity after accounting for taxonomic diversity) across th...     

Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed fores...     

Global patterns and ecological drivers of taxonomic and phylogenetic endemism in angiosperm generaOA

Endemism of lineages lies at the core of understanding variation in community composition among geographic regions because it reflects how speciation, extinction, and dispersal have influenced current distributions. Here, we investigated geographic patterns and ecological drivers of taxonomic and phylogenetic endemism of angiosperm genera across the world. We identify centers of paleo-endemism and neo-endemism of angiosperm genera, and show that they are mostly located in the Southern Hemisphere...     

Development of setal patterns in embryonic and adult aphids of the Hormaphidinae （Hemiptera： Aphididae）

The elementary traits and diversity of embryonic setal patterns of 31 species of 22 genera, in three tribes of Hormaphidinae are studied. The embryonic setal patterns to every species are provided. Based on the parsimony principle and the developmental principle, these patterns are analyzed in each tribe following the terminology of Richards （1965）. It is suggested that the setal patterns of abdominal tergites are the most important characters in embryonic and adult setal patterns. In conclusion, neoteny is a phylogenetic trend in the Hormaphidinae. Nipponaphidini and Hormaphidini have more typical neoteny in each genus and more diversity in different types of adult viviparous females than Cerataphidini, by showing more frequent and various protopatterns or mesopatterns.     

Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation

The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo-and pale...     

Latitudinal changes in species diversity of permafrost wetland plant communities in Great Xing’an Mountain valleys of Northeast China

Studying the changes of species diversity in plant communities along latitude gradients is important to discover the correlation between biodiversity and environmental factors. Along the main ridges of the Great Xing’an Mountains, 12 natural permafrost wetlands in the valleys were investigated from north to south. Latitudinal changes in species diversity were analyzed with regressive analysis. About 150 plant species were recorded and were found to be in the 12 permafrost wetland plant communities. Most plants belong to the Compositae or Gramineae. The number of family, genus and species increased significantly in the herb layer with decreasing latitude (P < 0.01), but decreased significantly in the shrub layer (P < 0.01). Species composition and the orders of dominant species in the plant communities by importance value changed along latitude. Latitudinal changes of α-diversity in permafrost wetland plant communities were different in the herb and shrub layers. With decreasing latitude, species richness and species diversity increased in the herb layer; but decreased in the shrub layer. The opposite patterns were found for species dominance. Species evenness in the shrub layer decreased with decreasing latitude. ?-diversity in the herb and shrub layers decreased first, and then increased, and finally decreased with increasing latitude. Species composition in the herb layer was similar among the plots at higher latitudes.     

Latitudinal changes in species diversity of permafrost wetland plant communities in Great Xing’an Mountain valleys of Northeast China

Studying the changes of species diversity in plant communities along latitude gradients is important to discover the correlation between biodiversity and environmental factors. Along the main ridges of the Great Xing’an Mountains, 12 natural permafrost wetlands in the valleys were investigated from north to south. Latitudinal changes in species diversity were analyzed with regressive analysis. About 150 plant species were recorded and were found to be in the 12 permafrost wetland plant communities. Most plants belong to the Compositae or Gramineae. The number of family, genus and species increased significantly in the herb layer with decreasing latitude (P < 0.01), but decreased significantly in the shrub layer (P < 0.01). Species composition and the orders of dominant species in the plant communities by importance value changed along latitude. Latitudinal changes of α-diversity in permafrost wetland plant communities were different in the herb and shrub layers. With decreasing latitude, species richness and species diversity increased in the herb layer; but decreased in the shrub layer. The opposite patterns were found for species dominance. Species evenness in the shrub layer decreased with decreasing latitude. ?-diversity in the herb and shrub layers decreased first, and then increased, and finally decreased with increasing latitude. Species composition in the herb layer was similar among the plots at higher latitudes.     

Estimating ancestral distributions of lineages with uncertain sister groups： a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. （Sapindaceae） including fossils

We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.     

Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe

Biological nitrogen fixation through prokaryotic microbe is an important source of nitrogen been input into many natural ecosystems. In this study the active diazotrophic community was investigated in the three treatments of mowed, grazed and enclosed Leymus chinensis steppes in Hulunbeier grassland of Inner Mongolia by using approaches of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) and sequence analysis. The community structure and diversity of the bacterial groups from the different samples was further analyzed by using different techniques, such as statistical analysis and diversity index evaluation of the band patterns etc. The results showed that grazing activity significantly reduced the number of species and quantities of nitrogen-fixing microorganisms, as well as the nifH gene diversity. However, enclosed plots had the lowest diversity of nifH gene. While the highest one found in mowing plots. A total of 30 sequences representing 25 different sequence types were recovered from the DGGE gels after phylogenetic constructions. The results also revealed that most sequences were coming from Alphaproteobacteria of Proteobacteria, and characterized by sequences of members of Rhodobacter, Bradyrhizobium, Mesorhizobium, Rhodopseudomonas, Xanthomonas, Azospirillum, Gluconacetobacter, Methylobacterium and Methylocystis. Symbiotic nitrogen-fixers existed in grazing, mowing and enclosed plots accounted for 21.4%, 47.3% and 31.3% respectively in their dominant nitrogen-fixing bacteria. The result of principal components analysis showed that the influence of different land use patterns on nitrogen-fixing microbial communities composition can be ordered as grazing plots > enclosed plots > mowing plots. Nitrogen-fixing microbial communities in L. chinensis steppe were significantly (P < 0.05) influenced by the levels of nitrate nitrogen, total phosphorus, available phosphorus contents and pH value when canonical correspondence analysis was employed to identify relationship between nifH gene and soil physicochemical factors under different land use patterns. The result obtained from correlation analysis showed that there was a significant (P < 0.05) negative relationship between the nitrate nitrogen and the total phosphorus content, furthermore, the available phosphorus content was strongly correlated (P < 0.01) with the pH value.     

Phylogenetic relationship of 16 Oedipodidae species （Insecta： Orthoptera） based on the 16S rRNA gene sequences

The sequences of the mitochondrial 16S rRNA gene of 16 Oedipodidae species were amplified and sequenced. All sequences were aligned and analyzed and the phylogenetic relationships were inferred. The properties of 16S gene in Oedipodidae showed typical patterns of many insects such as a high A＋T content and variable distance-dependent transition/transversion ratios. The 0.2 weight for sites of loops may be advisable for phylogeny reconstruction using the maximum parsimony method. The phylogenetic analysis results do not support the current subfamily classification systems of Oedipodidae. Bryodemellinae and Bryodeminae are closely related and should be merged as one subfamily. The status of Oedipodinae and Locustinae is also problematic.     

Genetic diversity and inferred ancestry of Asian lotus(Nelumbo nucifera) germplasms in Thailand and VietnamOA

Tropical lotus(Nelumbo) is an important and unique ecological type of lotus germplasm.Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization.Using 42 EST-SSR(expressed sequence tag-simple sequence repeats) and 30 SRAP(sequence-related amplified polymorphism) markers,we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam.In total,164 and 41 polymorphic ...     

Global patterns of phylogenetic diversity and transmission of bat coronavirus

Bats are reservoirs for multiple coronaviruses(Co Vs). However, the phylogenetic diversity and transmission of global bat-borne Co Vs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat Co V Rd Rp gene sequences to study the phylogenetic diversity and transmission of bat-borne Co Vs and the underlying driving factors. We found that host-switching events occurred more frequently for α-Co Vs than for β-Co Vs, and the latter was highly constrained by ...     

In silico Analysis of Sequential,Structural and Functional Diversity of Wheat Cystatins and Its Implication in Plant Defense

Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases.Cereal crops like wheat are continuously threatened by a multitude of pathogens,therefore cystatins offer to play a pivotal role in deciding the plant response.In order to study the need of having diverse specificities and activities of various cystatins,we conducted comparative analysis of six wheat cystatins(WCs) with twelve rice,seven barley,one sorghum and ten corn cystatin sequences employing different bioinformatics tools.The obtained results identified highly conserved signature sequences in all the cystatins considered.Several other motifs were also identified,based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering.Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins.Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs.Thus there is a significant conservation at the sequential and structural levels;however,concomitant variations maintain the functional diversity in this protein family,which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.     

The identity of Dinochloa species and enumeration of Melocalamus(Poaceae:Bambusoideae) in ChinaOA

Three woody bamboo species collected in Hainan,China in 1940 have been described as Dinochloa based on vegetative specimens.However,the identity of these species has long been in doubt,largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus,a climbing or scrambling bamboo genus of the paleotropical woody bamboos(Poaceae:Bambusoideae)that consists of about 15 species and one variety.To determine the phylogenetic affinity of the thr...     

Epidemiological and etiological investigation of dengue fever in the Fujian province of China during 2004–2014

Dengue fever(DF) is a vector-borne disease and a tremendous socioeconomic burden on tropical and subtropical countries worldwide. To explore the characteristics of DF epidemic in the Fujian province, information of DF cases in Fujian during 2004–2014 was collected and analyzed. The complete E genes of 48 viral isolates were amplified and sequenced for phylogenetic analysis. A total of 733 cases was reported, of which 612(83.5%) occurred during the peak period from August to October. Additionally, 76%(190/250) of imported cases originated from Southeast Asia countries, by the epidemiological investigation. Phylogenetic analysis of the 48 viral isolates revealed that three genotypes(I, IV, V) of DENV1, and one genotype each of DENV2(cosmopolitan) and DENV3(I) circulated in Fujian during 2004–2014. Similar to the results of the epidemiological investigations, the source of most of the viral isolates, including imported and indigenous cases, may be Southeast Asia countries; however, importation from adjacent provinces was also observed in recent years. Overall, DF is considered an imported epidemic disease in Fujian. Increasing diversity of the viral source and geographic expansion of the area affected by DF in recent years highlights the necessity for strengthening surveillance of the DF epidemic and developing strategies for DF prevention and control in Fujian.     

Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea(Zingiberaceae)OA

Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae,which consists of two disjunct groups in geography,namely the "Chinese" clade and the "Himalayan" clade.Despite extensive research on the genus,Roscoea species remain poorly defined and relationships between these species are not well resolved.In this study,we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes f...     

Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylo? genetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unsealed genera of Entomobryinae.