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Many species of the subfamily Polygonoideae are economically important. However, phylogenetic relationships and taxonomic treatments of these species remain disputed. In this study, we used highly orthologous nuclear genes and plastome sequence variation extracted from transcriptomes from 98 species of 26 genera of Polygonaceae mainly from the subfamily Polygonoideae to construct a robust phylogeny. We discerned six successively diverged and well‐defined clades and both nuclear and plastome phylogenies are highly consistent with each other in this subfamily. Phylogenetic relationships between all clades and subclades were well resolved within Polygonoideae. Our analyses revealed that the shrub tribe Atraphaxideae and the herbal genera Polygonum, Persicaria, and Fallopia are polyphyletic. The sampled species of Polygonoideae started to diversify around the Cretaceous/Tertiary boundary (70 Ma) when the global climate exhibited large oscillations. Further origins of more herbal and woody species were found to have clearly increased during later climatic oscillations. We found that woody habits, especially shrubs, originated multiple times from ancestral herbs in this subfamily. Local dry climates may have favored such habit shifts from ancestral herbs. Our results deepen our understanding of evolutionary diversification of Polygonoideae. [ABSTRACT FROM AUTHOR]

Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt‐resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re‐sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single‐copy nuclear genes from the whole genome recovered six well‐supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single‐copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus. [ABSTRACT FROM AUTHOR]

The development of next‐generation sequencing technologies allows researchers to address complex problems in species delimitation, especially for non‐model organisms. The taxonomic status of North American Nyssa species has long been debated and remains controversial. To elucidate the genetic structure and phylogenetic relationships of the five currently recognized North American Nyssa species, we conducted whole‐genome sequencing of representative individuals and identified genome‐wide single‐nucleotide polymorphisms (SNPs) by utilizing the recently released chromosome‐level assembly of Nyssa sinensis genome. Population genetic and phylogenetic analyses consistently inferred four well‐supported genetic clusters from our sampled individuals, that is, N. aquatica, N. ogeche, N. sylvatica, and N. biflora–N. ursina. Although the identification of N. biflora and N. ursina is primarily based on the morphological characteristics of leaves and drupes, the present evidence, including our principal components analysis of leaf morphological traits, strongly supports the taxonomic designation of N. biflora and N. ursina as a single species. In addition, these four genetic clusters were grouped into two major clades, that is, clade 1 (N. aquatica and N. ogeche) and clade 2 (N. sylvatica and N. biflora–N. ursina). Despite the fact that no evidence of widespread gene flow was found between these two major clades, our analyses revealed the possibility of introgression from N. sylvatica into N. biflora, albeit at a relatively low frequency. This study demonstrates the use of whole‐genome sequences as a promising avenue for delimiting species boundaries and further advocates for an integrative approach in the assessment of species delimitation. [ABSTRACT FROM AUTHOR]

A new AgOTf‐catalyzed domino reaction of 2‐alkynylbenzaldehyde and 4‐amino‐1‐methyl‐3‐propyl‐1H‐pyrazole‐5‐carboxamide has been reported via a sequential condensation, cyclization, and acetylenic hydroamination process. The developed protocol provides an efficient and modular access to a range of new fused tetracyclic heterocycle 6‐aryl‐9‐methyl‐11‐propyl pyrazolo[4′,3′:4,5]pyrimido[2,1‐a]isoquinolin‐8(9H)‐ones with two new rings in good yields. [ABSTRACT FROM AUTHOR]

A CuI/L‐proline‐catalyzed reaction of 2‐(2‐bromophenyl)‐4,5‐diaryl‐1H‐imidazole and potassium ethylxanthate unexpectedly gave bis(2‐(4,5‐diaryl‐1H‐imidazol‐2‐yl)phenyl)sulfane derivatives in high yields, rather than 2,3‐diphenyl‐5H‐benzo[e]imidazo[1,2‐c]thiazine‐5‐thione. This cascade procedure provided an efficient method to synthesize diphenylsulfanes using potassium ethylxanthate as a new type of sulfur source via the Csp2S bond Ullmann reaction twice. [ABSTRACT FROM AUTHOR]

The Qinghai–Tibet Plateau (QTP) sensu lato (sl) houses an exceptional species diversity in Asia. To develop a comprehensive understanding of species diversity in this fascinating region, we reviewed recent progress from biogeographic, paleogeographic, paleontological and genomic research of both plants and animals in the QTPsl. Numerous studies have been conducted to examine whether the QTPsl uplift triggered the production of rich species diversity there, whether a Quaternary "unified ice sheet" eliminated plants and animals on the central plateau and how high‐altitude species developed the extreme environment adaptations. Major disputes arose about the first issue, mainly from different understanding of the QTP circumscriptions and related uplift, inaccurate dating of molecular phylogenetic trees, and non‐causal correlations between uplift and species diversification. The QTPsl uplift is spatially and temporally heterogeneous, and abundant fossils reported recently similarly support such an asynchronous upheaval model across the entire region. Available phylogeographic studies of alpine plants and animals suggested their glacial refugia in the central QTPsl, rejecting a unified ice sheet during the Last Glacial Maximum. Genomic evidence from a limited number of alpine species has identified numerous candidate genes for high‐altitude adaptation. In the future, more studies should be focused on speciation and adaptation mechanisms of the alpine species in the QTPsl based on the cutting‐edge methods. [ABSTRACT FROM AUTHOR]

Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae. [ABSTRACT FROM AUTHOR]

Accurate species delimitation is fundamental to biodiversity conservation. The endangered spruce Picea brachytyla (Franch.) E. Pritz. was suggested to be polyphyletic based on a limited number of samples in previous studies. To evaluate polyphyly of P. brachytyla, we sampled 139 individuals from 16 populations across most of its distributional range, plus representatives of two related species, Picea likiangensis (Franch.) E. Pritz. and Picea wilsonii Mast. We sequenced 13 nuclear loci and three chloroplast and two mitochondrial loci for the following species delimitation. Phylogenetic analyses of nuclear loci grouped all individuals of P. brachytyla from Sichuan and Chongqing into one distinct lineage and those from Yunnan and Tibet (southern distribution) nested within the P. likiangensis species complex. Structure analyses confirmed this result. Networks of chloroplast DNA haplotypes similarly showed that P. brachytyla from the southern distribution nested within the P. likiangensis species complex, whereas haplotypes for the northern distribution comprised a separate and well‐supported lineage. These results suggest that P. brachytyla from the southern distribution is a part of the P. likiangensis species complex and should be removed from P. brachytyla. Our study highlights the utility of population genetic evidence in delimitating endangered species and understanding the conservation status of such species. [ABSTRACT FROM AUTHOR]

A silver‐catalyzed protocol for [3+1+1] annulation of nitrones and isocyanoacetates is reported. The reaction is proposed to proceed through sequential [3+2] cycloaddition, ring‐opening, cyclization‐oxidation, and dealkylation, allowing access to a broad scope of valuable polysubstituted imidazoles in high yields. [ABSTRACT FROM AUTHOR]

An unprecedented copper‐catalyzed heteroaromatization/sulfonyl transfer of propargylic alcohols with isocyanide has been developed. 3‐Sulfonyl benzofurans and indoles were produced under Cu(I) catalysis in good to high yields. The developed catalytic methodology provides controlled, modular, and facile access to sulfonyl benzoheterocycle scaffolds. [ABSTRACT FROM AUTHOR]

Aldehyde could undergo not only the subsequent condensation and cyclization with 2‐aminothiophene‐3‐carboxamide to build a pyrimidine ring, but also a Friedel‐Crafts alkylation reaction with thiophene moiety to give unexpected 6‐benzyl‐2‐arylthieno[2,3‐d]pyrimidin‐4(3H)‐ ones in good yields catalyzed by concentrated HCl. [ABSTRACT FROM AUTHOR]

As the well known biodiversity hotspot of the alpine plants in the world (Sun et al., 2017), many studies have been conducted on evolutionary origin and ecological adaptation of those species occurring in the QTP (e.g., Wen et al., 2014, 2019; Zhang et al., 2019). The Qinghai-Tibet Plateau (QTP) comprises a platform (sometimes called the Qinghai-Tibet Plateau I sensu stricto i ), the Himalayas, and Hengduan Mountains (Liang et al., 2018; Mao et al., 2021). Tong et al. (2021) reviewed the reproductive strategies of animal-pollinated alpine plants on the QTP, involving pollination system, pollen limitation, self-pollination, and sexual system. Paleobotany for Ancient Flora of the QTP and Related Paleo-Altitude Paleontology provides direct evidence for ancient flora of the QTP and further evolution in both floral composition and altitude change with time. [Extracted from the article]

The subtribe Saussureinae is a highly speciose group with more than 600 species distributed in the Northern Hemisphere and is particularly species‐rich at the high mountains of central and eastern Asia. Saussurea and Jurinea are the two main genera described within the subtribe. However, up to 15 satellite genera are recognized in some recent taxonomic treatments with an analytical viewpoint. For the first time, we carried out a complete sampling to clarify generic boundaries based on a well‐resolved phylogeny of Saussureinae. We employed a Hyb‐Seq technique that targets 1061 nuclear conserved ortholog loci designed for Compositae. After a filtering of potential paralogs, 588 loci were retained to infer phylogenetic trees under concatenation and coalescence approaches. High branch support resolution was recovered at the generic level, but a non‐monophyletic pattern was detected for most of the genera as they are currently circumscribed. Accordingly, we propose a new generic delimitation based on the three main clades recovered in the backbone tree, which are also in agreement with morphological evidence: Dolomiaea, Saussurea, and Jurinea. Following this classification into three genera, 18 new combinations are proposed. This new genus delineation will be used as a basis for future evolutionary studies in the Saussureinae. [ABSTRACT FROM AUTHOR]

A protocol involving cooperative silver‐ and base‐catalyzed diastereoselective cycloaddition of nitrones with isocyanides is described, providing access to a wide range of 2‐imidazolinone derivatives with various functional groups as single diastereomers. Varying the base and temperature of the reaction allowed selective access to both diastereomers of the product. A plausible reaction mechanism is proposed and supported by DFT calculations. [ABSTRACT FROM AUTHOR]

A cascade reaction of 2‐alkynylbenzaldehydes and 2‐(4,5‐diphenyl‐1H‐imidazol‐2‐yl)aniline was treated in DMF catalyzed by AgOTf leading to 6,13,14‐triaryl‐11bH‐imidazo[1,2‐c] isoquinolino[2,1‐a]quinazolines in high yields. This Domino reaction included condensation, cyclization, and acetylenic hydroamination under mild conditions to build fused pentacyclic heterocycle with three new bonds and two new rings. [ABSTRACT FROM AUTHOR]

A novel method for the synthesis of dibenzo[b,f]imidazo[1,2‐d][1,4]oxazepine derivatives was described via cascade Csp2N and Csp2O bond constructions. It was a crossed double Ullmann reactions using 4,5‐diaryl‐2‐(2‐hydroxylphenyl)‐1H‐imidazole as the double nucleophilic centers in the presence of Cs2CO3, while 1‐bromo‐2‐iodobenzene was used as a substrate catalyzed by CuI and o‐phenanthroline in good yields. [ABSTRACT FROM AUTHOR]

"Sky island" species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands. [ABSTRACT FROM AUTHOR]

2‐Bromobenzoic acids underwent an α‐arylation with cyclohexane‐1,3‐diones to give 1H‐benzo[c]chromene‐1,6(2H)‐diones under Ar atmosphere catalyzed by CuI/l‐proline in the presence of Cs2CO3. The subsequent regioselective oxidation took place under O2 balloon automatically based on the substituents for the construction of structurally diversified benzo[c]coumarin derivatives. [ABSTRACT FROM AUTHOR]

A silver‐induced cycloaddition of isocyanides with acyl chlorides has been developed. This transition metal‐catalyzed strategy provides an effective and scalable approach for the formation of 2,5‐disubstituted oxazoles in good to high yields. The employed silver‐based MOF catalyst can be efficiently recycled without compromising the yield. [ABSTRACT FROM AUTHOR]

Betulaceae is a well‐defined family of Fagales, including six living genera and more than 160 modern species. Species of the family have high ecological and economic value for the abundant production of wood. However, phylogenetic relationships within Betulaceae have remained partly unresolved, likely due to the lack of a sufficient number of informative sites used in previous studies. Here, we re‐investigate the Betulaceae phylogeny with whole chloroplast genomes from 24 species (17 newly assembled), representing all genera of the family. All the 24 plastomes are relatively conserved with four regions, and each genome is ∼158–161 kb long, with 111 genes. The six genera are all monophyletic in the plastome tree, whereas Ostrya Scop. is nested in the Carpinus clade in the internal transcribed spacer tree. Further incongruencies are also detected within some genera between species. Incomplete lineage sorting and/or hybrid introgression during the diversification of the family could account for such incongruencies. Our dating analysis, based on four fossils, suggests that the most recent common ancestors of the extant genera date back to the mid‐ to late Miocene, and confirms that Betulaceae started to diversify in the upper Cretaceous/early Paleocene. Our results highlight the significance of using more informative sites in resolving phylogenetic relationships. Plastome data and increased taxon sampling will help to better understand the evolutionary history of Betulaceae in the future. [ABSTRACT FROM AUTHOR]

Accurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes. [ABSTRACT FROM AUTHOR]

A silver‐catalyzed cycloaromatization of 1‐(2‐ethynyl‐phenyl)‐prop‐2‐yn‐1‐ol with isocyanides efficiently provides benzo[b]fluorene and benzofuran‐pyrrole derivatives through a modular cascade reaction that includes a nucleophilic attack on the diyne substrate. A C−C cross‐coupling/oxygen transportation/Diels‐Alder/hydrogen shift/isomerization cascade mechanistic pathway is proposed. [ABSTRACT FROM AUTHOR]

The α‐arylation between cyanoacetate and 2‐(2‐bromophenyl)‐1H‐perimidine took place first catalyzed by CuI/L‐proline in the presence of NaHCO3, and then the amino on perimidine chemoselectively attacked the cyano group to undergo a nucleophilic addition, giving a series of 13‐aminoisoquinolino[2,1‐a]perimidine‐12‐carboxylate derivatives in good yields. [ABSTRACT FROM AUTHOR]

A consecutive condensation, cyclization, and dehydration of 2‐(1H‐benzo[d]imidazol‐2‐yl) anilines and ketonic acid in toluene catalyzed by TsOH gave a series of benzo[4,5]imidazo [1,2‐c]pyrrolo[1,2‐a]quinazolin‐3(2H)‐one derivatives in good to high yields. The structure of 3e was further confirmed unambiguously by X‐ray diffraction analysis. [ABSTRACT FROM AUTHOR]

The chemo‐selective reaction of 2‐amino‐N′‐arylbenzohydrazide and ketonic acid catalyzed by iodine was used to synthesize various 2,3‐dihydroquinazolin‐4(1H)‐ones efficiently. The use of levulinic acid furnished a series of 2,3,3a,4‐tetrahydropyrrolo[1,2‐a]quinazoline‐1,5‐diones in high yields, while acetobutyric acid only afforded the quinazoline skeletons without forming the second pyridine ring. Using alcohol as the solvent instead of ionic liquids, a subsequent esterification was performed with the carboxylic group of acetobutyric acid substrate in one‐pot manner. [ABSTRACT FROM AUTHOR]

Both hybridization and intraspecific morphological variation across environmental gradients complicate species delineation. We aimed to discern both possibilities that may blur species boundaries in the Carpinus viminea–Carpinus laxiflora–Carpinus londoniana species complex. We conducted statistical analyses on 535 specimens encompassing the entire distribution of this species complex to identify phenotypic clusters. Additionally, we analyzed genetic divergence and probable hybridization between clusters using 76 individuals from 37 populations. Based on phenotypic and genetic clusters, we tentatively recognized four species: C. viminea, C. fargesii, C. laxiflora, and C. londoniana. Except for rare overlapping distributions between C. fargesii and C. londoniana, the redefined four species are mostly allopatric to each another based on their distributions. The morphological delimitation, species boundary and distribution of each species differ distinctly from past taxonomic treatments. For example, specimens previously identified under C. viminea, in fact, belong to three different species. Hybrids between C. fargesii and C. londoniana exhibit morphological traits similar to C. viminea, thereby contributing to difficulties in determining species boundaries and outlining species distributions. These findings suggest that local selection and geographical isolation may together have promoted both phenotypic and genetic divergences within this species complex. However, interspecific hybridization blurs species boundaries by producing hybrids with phenotypic similarity in addition to intraspecific variation. This study emphasizes the importance of statistical analyses of population‐level morphological and genetic variations across major distributional ranges for an integrative delimitation of species boundaries and the identification of hybridization and hybrids. [ABSTRACT FROM AUTHOR]

Abstract: The halophyte model plant Eutrema salsugineum (Brassicaceae) disjunctly occurs in temperate to subarctic Asia and North America. This vast, yet extremely discontinuous distribution constitutes an ideal system to examine long‐distance dispersal and the ensuing accumulation of deleterious mutations as expected in expanding populations of selfing plants. In this study, we resequenced individuals from 23 populations across the range of E. salsugineum. Our population genomic data indicate that E. salsugineum migrated “out of the Altai region” at least three times to colonize northern China, northeast Russia and western China. It then expanded its distribution into North America independently from northeast Russia and northern China, respectively. The species colonized northern China around 33.7 thousand years ago (kya) and underwent a considerable expansion in range size approximately 7–8 kya. The western China lineage is likely a hybrid derivative of the northern China and Altai lineages, originating approximately 25–30 kya. Deleterious alleles accumulated in a stepwise manner from (a) Altai to northern China and North America and (b) Altai to northeast Russia and North America. In summary, E. salsugineum dispersed from Asia to North America and deleterious mutations accumulated in a stepwise manner during the expansion of the species’ distribution. [ABSTRACT FROM AUTHOR]

2-(1 H-benzo[ d]imidazol-2-yl)anilines reacted with haloketones including 5-chloropentan-2-one and 6-chlorohexan-2-one catalyzed by iodine, giving benzo[4,5]imidazo[1,2- c]pyrrolo[1,2- a]quinazoline and 6 H-benzo[4,5]imidazo[1,2- c]pyrido[1,2- a]quinazoline derivatives, respectively. This domino-type reaction formed two new heterocycles and three new covalent bonds in one-pot procedure and provided a green method for the synthesis of fused pentacyclic heterocycles bearing both quinazoline and benzimidazole moieties in ionic liquids. [ABSTRACT FROM AUTHOR]

Two series of furo[3,2- f]quinoline-2-carboxylate were obtained via a three-component reaction of aldehydes, 5-aminobenzofuran-2-carboxylate, and 4-hydroxy-2 H-chromen-2-one or cyclopentane-1,3-dione in DMF under catalyst-free condition in high yields. This one-pot three-component reaction provided an efficient method for the synthesis of fused polycyclic heterocycles for bioactive screening. [ABSTRACT FROM AUTHOR]

With the advance of next-generation sequencing techniques, phylogenetic analyses based on genomic data are becoming frequent in plants. However, the efficacy of different methods used to retrieve orthologs for phylogenetic studies based on transcriptome sequences is rarely compared and examined for closely related species with low genetic differentiation. In this study, we used both low-copy gene-based approaches and mapping-based approaches to construct a phylogeny of Betulaceae. We found that both approaches showed no distinct differences in phylogeny construction and associated bootstrap support, although mapping-based methods seemed to be superior to the former in all analyses particularly when the summed length of orthologs was not long enough. Phylogenetic relationships within the family, largely consistent with those previously based on chloroplast DNA and nuclear internal transcribed spacer sequence variations, received high support for all clades and subclades. However, we found that support values for the sister relationship between two polyploid genera were lower than those between diploid groups if only a few orthologs were sampled. This may result from ortholog misidentification due to genome duplications. [ABSTRACT FROM AUTHOR]

As the highest and largest plateau in the world, the Qinghai-Tibet Plateau, with its numerous endemic species, is one of the important alpine biodiversity hotspots. Only recently have the evolutionary histories and underlying adaptations of these alpine plants become clear, through research mostly based on testable experiments and analyses. In this issue, we collected a total of 13 papers related to such aims. In addition, we selected a few published papers to highlight the major findings in the recent past. We also outlined the outlook and direction of future research. [ABSTRACT FROM AUTHOR]

It remains unknown how Ostryopsis intermedia B. Tian & J. Q. Liu (Betulaceae) originated in the SE Qinghai-Tibet Plateau (QTP). We examined sequence variations of two maternally inherited chloroplast (cp) DNA fragments and amplified fragment length polymorphisms (AFLP) of 32 populations for this species and two congeners, O. davidiana Decne. and O. nobilis Balf. f. W. W. Sm., distributed in northern China and the SE QTP. Each of the two distinct cpDNA haplotype groups was fixed by O. davidiana or O. intermedia, respectively, whereas both were found in O. nobilis. All analyses of AFLP suggested that O. intermedia is more closely related to O. davidiana than to O. nobilis and Bayesian clustering analysis ( K = 2) further suggested that the genomic composition of O. intermedia showed a slightly mosaic origin from the other two species, although mostly from O. davidiana. Analyses of AFLP indicated the highest nuclear genetic diversity for O. davidiana and lowest for O. intermedia. The origin of O. intermedia through hybrid speciation due to southward migration of O. davidiana and the following hybridization with O. nobilis may provide the most reasonable explanation for the inconsistency between phylogenetic relationships of three species and degrees of genetic diversity from cpDNA sequences or AFLP datasets. Ostryopsis intermedia may represent one more diploid hybrid species found in the QTP, although further strong tests are needed based on additional data. [ABSTRACT FROM AUTHOR]

Pleistocene climate change has had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium ( Brassicaceae), Pugionium cornutum and Pugionium dolabratum, which occupy different desert habitats in northwest China., We surveyed sequence variation for internal transcribed spacer ( ITS), three chloroplast (cp) DNA fragments, and eight low-copy nuclear genes among individuals sampled from 11 populations of each species across their geographic ranges., One ITS mutation distinguished the two species, whereas mutations in cp DNA and the eight low-copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China., Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium as a result of divergence in different habitats that formed in association with the expansion of deserts in China. [ABSTRACT FROM AUTHOR]

Parallel evolution provides an excellent framework to infer the genetic bases of adaptive traits and understand the importance of natural selection in shaping current biodiversity. The upper leaves of the 'glasshouse plants' transform into translucent bracts that show numerous adaptions in alpine habitats. It remains unknown whether similar molecular changes occur under the parallel bract evolution of different 'glasshouse' species. In this study, we compared the results on phenotypic and physiological differences and presented the results of cDNA-AFLP analyses of transcriptional changes between translucent bracts and normal leaves in Rheum alexandrae. We also examined the homologous candidate genes with the same expression changes between this species and another 'glasshouse' species, R. nobile. We found that bracts of R. alexandrae are similar to those of R. nobile in anatomical features: chloroplasts have degenerated and chlorophyll contents are greatly reduced, which suggests that foliar photosynthetic functions in bracts of both species have been reduced or totally altered. Among the 6000 transcript-derived fragments (TDFs) in bracts and leaves of R. alexandrae, 420 (7%) were differentially expressed (up- or downregulated) between bracts and normal leaves. There were a total of 13 homologous TDFs with the same expression changes between R. alexandrae and the previously studied R. nobile. Except for the two that were not functionally annotated, eight of the homologous TDFs were found to be involved in stress and defense responses whereas the other three were related to photosynthesis. The up- or downregulation of these candidate genes was highly congruent with anatomical characteristics and adaptive functions of the bracts found for 'glasshouse' plants. These findings suggested that the 'glasshouse' phenotypes may have common molecular bases underlying their parallel evolution of similar adaptive functions and highlighted the importance of the natural selection in producing such phenotypes. [ABSTRACT FROM AUTHOR]

Phylogeography has been one major focus of evolutionary biology in recent years, with many important advances in Chinese species. In this issue, we collected 11 phylogeographic studies of plants by Chinese laboratories. We further synthesized the main findings and patterns emerging from these and previous phylogeographic studies in China and asked where phylogeographic research should be directed in the coming years. Numerous examples have shown that phylogeographic patterns in China did not show an expected expansion-contraction pattern at large scale, mirroring the geological records showing that no unified ice sheet had developed in China during the Quaternary Period. Instead, regional expansions and intraspecific divergences are very common in most studied species during the Quaternary oscillations. Different intraspecific lineages or alleles (haplotypes) were detected in multiple localized refugia, from where regional or local expansions are likely to have started. Hybridizations and introgressions are frequent between intraspecific lineages or between different species. We also reviewed computational methods for phylogeographic analyses. Despite the great progress made in recent years, there remains much to discover about the spatial-temporal dimensions and underlying speciation mechanisms of Chinese plants. Phylogeographic studies represent a key knot that connects the genus phylogeny (macroevolution) and speciation and adaptation (microevolution). Therefore, we advocate that: (i) phylogeographic studies of plants in China should be directed to the closely related species or a monophyletic group (for example, a genus or a section) in the coming years; and (ii) population genetic data based on direct sequencing multiple loci, especially those from nuclear genome and statistical tests should be widely adopted and enforced. The recovered intraspecific divergences and phylogeographic patterns of multiple-species may allow us to better understand the high plant diversity in China and set up concrete hypotheses for studying plant speciation and diversification mechanisms in this region. [ABSTRACT FROM AUTHOR]

Phragmites australis is a cosmopolitan clonal species, but one haplotype from Eurasia has become highly invasive in North America. This article describes an investigation of the phylogeographic composition of 77 populations from China, based on the sequencing of two chloroplast non-coding DNA regions. A total of 11 haplotypes were detected, based on the sequence alignments of two chloroplast DNA fragments from 421 sampled individuals. Six of these haplotypes were completely new, and did not correspond to any of this species' 27 previously known haplotypes. The invasive haplotype M and haplotypes O and P were shown to occur frequently. Haplotype O is widely distributed across all regions and probably represents the primitive haplotype of this species. In contrast, P is mainly distributed in the humid eastern and northeastern regions of China, whereas M is more frequent in western and northwestern China-arid habitats with low precipitation. Between eastern and northeastern and western and northwestern regions, there was distinct genetic differentiation; the former region has a higher genetic diversity than the latter. The high occurrence of haplotype M in western China suggests that it prefers more arid habitats. These findings shed new light on the native distribution, adaptation, and habitat preference of haplotype M, which invaded North America. [ABSTRACT FROM AUTHOR]

The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis, a dominant species of the conifer forests in the eastern declivity of the Qinghai-Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species. In conifers, mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow. To this end, we examined the sequence variation of two mtDNA fragments ( nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments ( trnL-trnF, trnS-trnG and nadhK/C). We found that cpDNA probably introgressed from P. purpurea into remote populations of P. likiangensis through long-distance dispersal. Multiple refugia seem to have been maintained for P. likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions. Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations. However, genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions, which may result from the long-distance dispersal of the cpDNA, as well as its fast lineage sorting during intraspecific divergences. Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers, which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa. Together, the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion, long-distance dispersal, and intraspecific divergences at two sets of DNA genomes with different rates of gene flow. [ABSTRACT FROM AUTHOR]

Numerous temperate plants now distributed across Eurasia are hypothesized to have originated and migrated from the Qinghai-Tibet Plateau (QTP) and adjacent regions. However, this hypothesis has never been tested through a phylogeographic analysis of a widely distributed species. Here, we use Hippophaë rhamnoides as a model to test this hypothesis., We collected 635 individuals from 63 populations of the nine subspecies of H. rhamnoides. We sequenced two maternally inherited chloroplast (cp) DNA fragments and also the bi-paternally inherited nuclear ribosomal ITS., We recovered five major clades in phylogenetic trees constructed from cpDNA and internal transcribed spacer (ITS) sequence variation. Most sampled individuals of six subspecies that are distributed in northern China, central Asia and Asia Minor/Europe, respectively, comprised monophyletic clades (or subclades) nested within those found in the QTP. Two subspecies in the QTP were paraphyletic, while the placement of another subspecies from the Mongolian Plateau differed between the ITS and cpDNA phylogenetic trees., Our phylogeographic analyses supported an 'out-of-QTP' hypothesis for H. rhamnoides followed by allopatric divergence, hybridization and introgression. These findings highlight the complexity of intraspecific evolutions and the importance of the QTP as a center of origin for many temperate plants. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

Delayed selfing could provide ovules with an opportunity to be fertilized as a means of “pollination assurance” before the flowers wilt. It could, thus, be regarded as an adaptation to unpredictable pollinator environments. Within the alpine biennial Gentianopsis paludosa, the showy flowers and herkogamy at the early stage of a flower's life cycle may favor outcrossing. As the flower ages, anthers contact the central stigma due to the elongation of all filaments, resulting in autonomous selfing. Flower visitors are extremely rare in a high altitude population; and examination of the mating system indicates that G. paludosa is self-pollinated under natural conditions in this population. While at the lower altitude, the bumblebee visitation rate is relatively high but possibly unreliable. Stigma receptivity is the highest on the third day of anthesis, and decreases thereafter. Pollen viability is the highest when flowers open, and gradually decreases later. Self-pollination of G. paludosa occurs at the late stage of a flower's lifecycle when stigma receptivity and pollen viability have both decreased, suggesting delayed selfing and assurance of seed production. This delayed selfing could assure seed production under the constraints of pollinator scarcity, but ensure outcrossing when pollinators were available. Such a flexible pollination mechanism is highly adaptive in the alpine environment of the Qinghai-Tibetan Plateau. [ABSTRACT FROM AUTHOR]

To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau (QTP) responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades (A, B and C). Analysis of molecular variance (amova) revealed that most of the genetic variability was found within populations (0.693), while differentiations between populations were obviously distinct ( Fst= 0.307). Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago (kya) were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu's FS values and ‘ g’ tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum (LGM) and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages. [ABSTRACT FROM AUTHOR]

Recent work has suggested that rates of introgression should be inversely related to levels of gene flow because introgressed populations cannot be ‘rescued’ by intraspecific gene flow if it is too low. Mitochondrial and chloroplast DNA (mtDNA and cpDNA) experience very different levels of gene flow in conifers due to their contrasted maternal and paternal modes of transmission, hence the prediction that mtDNA should introgress more readily than cpDNA in this group. Here, we use sequence data from both mtDNA and cpDNA to test this hypothesis in a group of closely related spruces species, the Picea asperata complex from China. Nine mitochondrial and nine chloroplast haplotypes were recovered from 459 individuals in 46 natural populations belonging to five species of the Picea asperata complex. Low variation was found in the two mtDNA introns along with a high level of differentiation among populations ( GST = 0.90). In contrast, we detected higher variation and lower differentiation among populations at cpDNA markers ( GST = 0.56), a trend shared by most conifer species studied so far. We found that cpDNA variation, although far from being fully diagnostic, is more species-specific than mtDNA variation: four groups of populations were identified using cpDNA markers, all of them related to species or groups of species, whereas for mtDNA, geographical variation prevails over species differentiation. The literature suggests that mtDNA haplotypes are often shared among related conifer species, whereas cpDNA haplotypes are more species-specific. Hence, increased intraspecific gene flow appears to decrease differentiation within species but not among species. [ABSTRACT FROM AUTHOR]