Phylogenetics and evolution of phyllotaxy in the Solomon's seal genus Polygonatum (Asparagaceae: Polygonateae)

Polygonatum is the largest and most complex genus in tribe Polygonateae, comprising approximately 57 species widely distributed in the warm temperate, subtropical and boreal zones of the Northern Hemisphere. However, phylogenetic relationships in the genus remain poorly understood. The objectives of this study were to reconstruct the phylogenetic relationships of the genus using four plastid markers, and to examine the evolution of leaf arrangement in Polygonatum in the phylogenetic context of its closely related taxa. Thirty Polygonatum species were sampled to infer phylogenetic relationships using maximum‐likelihood and Bayesian analyses. The evolution of leaf arrangements was reconstructed using Bayesian, parsimony and likelihood methods. The phylogenetic analyses supported the current generic delimitation of Polygonatum, with Heteropolygonatum recognized as a distinct genus. Three major lineages in Polygonatum were well supported, largely correlated with geographical distribution and the most recent classification at the sectional level. However, our results did not support the currently recognized series, especially the two large series Verticillata and Alternifolia. Bayesian analyses support the alternate‐leaf arrangement as the ancestral state for Polygonatum, but parsimony and maximum‐likelihood analyses suggest an equivocal state for crown Polygonatum. Leaf arrangement was found to be evolutionarily labile. A new nomenclatural combination was made: P olygonatum section S ibirica (L.I.Abramova) Y.Meng, comb. nov. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 435–451.     

A cytotaxonomic analysis of Chinese Polygonatum (Asparagaceae) species

Chromosome numbers and karyotype data of 19 Chinese Polygonatum species generated from 51 populations are presented in this paper. Karyograms of P. cirrhifoliodes, P. gracile, P. hookeri, P. jinzhaiense and P. nodosum are reported for the first time. The chromosome numbers 2n = 28 for P. hookeri and 2n = 60 for P. zanlanscianense are reported for the first time. Satellite chromosomes in the analyzed Polygonatum species can be classified into nine types with respect to the position of secondary constrictions. The occurrence of these types correlates with the infrageneric classification. Karyotypes are bimodal in most Polygonatum species. Polyploidy is common in Polygonatum, and polyploid taxa exhibit higher karyotype asymmetry.     

Karyotypes of 16 populations of eight species in the genus Polygonatum (Asparagaceae) from China

The karyotypes of 16 populations belonging to eight species of Polygonatum from China were analysed. The chromosome numbers and karyotypes of P. omeiense, P. adnatum and P. hirtellum and the diploidy of P. tessellatum are reported for the first time. The basic chromosome numbers were x = 11, 13, 14 and 15. Based on Stebbins' karyotypic classification, the four karyotypes were recognized as 2B, 3B, 2C and 3C. Considering the arm ratio and individual chromosome size, it was concluded that the possible evolutionary trend of the karyotypes in Polygonatum was from 2B to 3C. The results show that: (1) satellite heterozygosity occurs in many species of this genus; (2) mixoploidy and B chromosomes occur in some species; and (c) karyotypes are different in different species and even in different populations of the same species. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 245–254.     

GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES,RHODOPHYTA)1

We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR‐RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS‐1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR‐RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains.     

Research Note: Simple molecular discrimination of cultivated Porphyra species (Porphyra yezoensis and Porphyra tenera) and related wild species (Bangiales,Rhodophyta)

To discriminate between cultivated Porphyra species (Porphyra yezoensis and Porphyra tenera) and closely related wild Porphyra species, we developed a polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) analysis of the rbcL gene using five restriction enzymes. Although our previous PCR‐RFLP analyses of internal transcribed spacer (ITS) rDNA and plastid RuBisCO spacer regions could not always discriminate wild P. yezoensis, wild P. tenera, and closely related wild species, the PCR‐RFLP profiles of the rbcL gene were useful in discriminating samples collected from natural habitats. Therefore, PCR‐RFLP analysis of the rbcL gene will help in the simple identification of a large number of samples, not only for the establishment of reliable cultures as breeding material, but also for the taxonomic investigations of species that are closely related to cultivated Porphyra.     

Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)

Introgression can introduce novel genetic variation at a faster rate than mutation alone and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expand our local ancestry analysis to the whole genome of both parents to provide a comprehensive view of introgression patterns and to identify additional candidate regions for adaptive introgression genomewide. Populus trichocarpa is a large, fast‐growing tree of mild coastal regions of the Pacific Northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter cold. The species hybridize where they are parapatric. We detected asymmetric patterns of introgression across the whole genome of these two poplar species adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals contained more genomic regions with unusually high levels of introgression (19 regions) and also the largest introgressed genome fragment (1.02 Mb) compared with admixed P. balsamifera (nine regions). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles in survival and adaptation. Furthermore, we detected a potential overrepresentation of subtelomeric regions in P. balsamifera introgressed into P. trichocarpa and possible protection of sex‐determining regions from interspecific gene flow.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Pollination system of the Pilosocereus leucocephalus columnar cactus (tribe Cereeae) in eastern Mexico

It has been suggested that there is a geographic dichotomy in the pollination systems of chiropterophilous columnar cacti: in intra‐tropical areas they are pollinated almost exclusively by bats, whereas in extratropical areas they are pollinated by bats, birds and bees. However, currently the studies are clumped both taxonomically (mainly Pachycereeae species) and geographically (mainly in the Tehuacan Valley and the Sonoran Desert). This clumping limits the possibility of generalising the pattern to other regions or cactus tribes. Only four of the 36 chiropterophilous cacti in Pilosocereus have been studied. Despite the tropical distribution of two Pilosocereus species, bees account for 40–100% of their fruit set. We examined how specialised is the pollination system of P. leucocephalus in eastern Mexico. As we studied tropical populations, we expected a bat‐specialised pollination system. However, previous studies of Pilosocereus suggest that a generalised pollination system is also possible. We found that this cactus is mainly bat‐pollinated (bats account for 33–65% of fruit set); although to a lesser degree, diurnal visitors also caused some fruit set (7–15%). Diurnal visitors were more effective in populations containing honeybee hives. P. leucocephalus is partially self‐compatible (14–18% of fructification) but unable to set fruit without visitors. Despite the variation in pollination system, P. leucocephalus shows more affinity with other columnar cacti from tropical regions than with those from extratropical regions. Although we report here that a new species of tropical Pilosocereus is relatively bat‐specialised, this Cereeae genus is more flexible in its pollination system than the Pachycereeae genera.     

Oral yeast flora and its ITS sequence diversity among a large cohort of medical students in Hainan,China

The most prevalent fungal infection of humans is candidiasis which is caused by species of Candida that are typical members of the commensal microbial flora of the oral mucosa and other body surfaces. Since species of Candida differ in virulence properties and susceptibilities to anti-fungal drugs, understanding the human commensal yeast flora will have a significant impact on designing treatment and prevention strategies against yeast infections. However, although there is a global interest in Candida species, the global distributions of Candida species remain largely unknown, especially among healthy hosts. Here we report the oral yeast flora from the surveys of over 1,000 medical students in China. Our results showed that this population had a yeast carriage rate (4.5%) much lower than other population samples reported previously from Mainland China (40–70%). In addition, C. albicans was isolated at a much higher frequency than those from other Chinese samples, with a frequency (80.9%) more similar to those in developed regions such as North America. The oral yeast carriage rates and yeast species compositions were similar between male and female students and between the hosts borne and raised on Hainan Island and those borne and raised on Mainland China. Furthermore, the sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster was analyzed for strains of the dominant species, C. albicans. Our analysis identified 14 ITS types among the 41 Hainan isolates of C. albicans. However, only four of the 14 ITS types were identical to those in reference strains from Europe and North America. Taken together, our analyses suggest that the oral yeast flora among host populations in China is highly heterogeneous and that there is a high ITS sequence diversity in the Hainan population of C. albicans.     

Characterization of Botryosphaeria dothidea and Lasiodiplodia pseudotheobromae from English Walnut in China

China is the largest walnut producer in the world, and walnut trees, especially English walnut, are widely distributed in the country. Species of Botryosphaeriaceae include important plant pathogens that can cause diseases on many tree crops including English walnut. Recently, disease symptoms caused by Botryosphaeriaceae were observed on English walnut branches or kernels from Beijing, Henan and Sichuan provinces in China. Based on morphological characteristics and phylogenetic analyses of the ITS rDNA sequences and translation elongation factor 1‐alpha (TEF‐1α) gene regions, Botryosphaeria dothidea and Lasiodiplodia pseudotheobromae were identified. Pathogenicity tests showed that both species are virulent to English walnut. To our knowledge, this is the first report of L. pseudotheobromae infecting English walnut in the world.     

Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.     

Leaf life span as a simple predictor of evergreen forest zonation in China

Aim Our aim was to investigate how the average life span of canopy leaves might be used to predict the geographical distribution of natural forests at large geographical scales, and to explore the link between leaf characteristics and ecosystem functioning. We examine whether there is a general relationship between canopy mean leaf life span and climate (i.e. temperature and precipitation) that can be used to predict evergreen forest zonation in China. Location Forest areas in China. Methods During July and August of 2002–2004, we conducted a latitudinal forest transect spanning about 30° of latitude in eastern China. The canopy mean leaf life span was calculated to include all tree species (groups) in each forest plot through weighted averages scaled up from branch‐level measurements. Data from our previous work conducted in the Tibetan Alpine Vegetation Transects (TAVT) and from other investigators were compiled to supplement our results. Based on regression equations developed on the pooled data, and using gridded temperature and precipitation datasets, we simulated the distribution of canopy mean leaf life span for forests in China. The predicted leaf life span zonation was compared with a map of Chinese forest vegetation divisions published in 1980. Results Canopy mean leaf life span across 10 evergreen forest plots in eastern China showed a decreasing trend as mean annual temperature increased, following a common logistic pattern consistent with the data from the TAVT and other investigators. In pooled data for 40 evergreen forest plots across tropical and boreal regions, canopy mean leaf life span generally showed a negative relationship with mean annual temperature (r² = 0.72, P < 0.001), and a positive correlation with mean annual precipitation where mean annual temperature was > 8°C (r² = 0.45, P < 0.01). The climate‐based simulations of leaf life span zonation compared well with the previously published boundaries of forest vegetation divisions in eastern China. Main conclusions Our results reveal that mean leaf life span in evergreen forests follows a common logistic pattern associated with mean annual temperature and precipitation, which can in turn be used to predict evergreen forest zonation in eastern China.     

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of R_st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G_st = 0.712) among populations. A high G_st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.     

中国腹枝衣属地衣的多样性与区系研究

为探讨中国腹枝衣属地衣的物种多样性,进一步明确其分布特征与种类组成,该研究通过野外调查及采集地衣标本,结合形态、解剖、化学等方法,对128份采自中国热带及亚热带地区多个省份的腹枝衣属(Herpothallon)地衣标本进行了分类鉴定,共鉴定出腹枝衣属地衣12种,其中南方腹枝衣 [H. australasicum (Elix)Elix & G. Thor]、颗粒腹枝衣(H. granulosum Jagadeesh Ram & G. P. Sinha)、喜马拉雅腹枝衣(H. himalayanum Jagadeesh & G. P. Sinha)、裂芽腹枝衣(H. isidiatum Jagadeesh Ram & G. P. Sinha)和小腹枝衣(H. minutum Jagadeesh)为中国新记录种。并且对该属所有已知(已报道和本次鉴定)种类进行综合分析。结果表明:(1)中国已知腹枝衣属地衣14种,占世界已报道种类的29.17%。(2)地理成分有5种类型,即泛热带分布、热带亚洲至热带澳大利亚分布、热带亚洲和热带美洲间断分布、热带亚洲分布和中国特有分布。(3)中国腹枝衣属地衣主要分布在海拔300～2 500 m的范围内。(4)生长基物多为树皮,叶生、石生和藓生的物种较少。该研究结果表明,中国南方腹枝衣属地衣的物种多样性较高,这对明确中国该属地衣物种组成以及地衣多样性保护具有重要意义。     

Updating the knowledge of assassin bug cockroaches (Blattodea: Blaberidae: Paranauphoeta Brunner von Wattenwyl): Species from China and taxonomic changes

The investigation into the cockroach genus Paranauphoeta Brunner von Wattenwyl is insufficient, and there is a lack of taxonomic documentation of this genus from China. Recently, the authors obtained some newly collected specimens which facilitated this study. In this paper the generalized morphology of Paranauphoeta is interpreted in detail, particularly for the male phallic complex, which is illustrated as a whole rather than in pieces. The taxonomy of Paranauphoeta species from China is revised. One out of four species recorded from China, P. indica Saussure & Zehntner, is removed; instead, P. kirby nom. nov. is recorded from China. Together with three new species described in this paper, namely, P. anulata sp. nov. , P. brachyptera sp. nov. and P. lineola sp. nov. , a total of seven Paranauphoeta species are now known to occur in China, whose habitus photos are provided. The new species confirm that this genus is wing‐polymorphic. Male structures, if available, are illustrated. Female structures and oothecae, of which knowledge is limited in this genus and also in cockroach taxonomy, are illustrated or documented, respectively. A key to and a distribution map of the Paranauphoeta species from China are provided. In addition, P. atra Shelford nom. rev. , P. sinica Bey‐Bienko stat. nov. and P. vietnamensis Anisyutkin stat. nov. are regarded as valid separate species.     

Phytochemical constituents and chemotaxonomic study of Polygonatum prattii Baker

Fifteen compounds were obtained from Polygonatum prattii Baker, which could be divided into four steroids, nine flavonoids, one lignanoid and one acidamide. The chemotaxonomic significance of P. prattii and the some other species among Asparagaceae was also discussed. As a result, Polygonatum may have close relationships with Liriope, Disporopsis, Ophiopogon and Aspidistra. Additionally, homoisoflavanones and steroids can be recognized as typical biomarkers for the above genus.     

The speciation history of northern‐ and southern‐sourced Eranthis (Ranunculaceae) species on the Korean peninsula and surrounding areas

The temporal and spatial origins and evolution of the genus Eranthis have not been previously studied. We investigated the speciation and establishment histories of four Eranthis species: Eranthis byunsanensis, E. pungdoensis, E. stellata, and E. pinnatifida. The sampling localities were Korea, Japan, Jilin in China, and the area near Vladivostok in Primorskiy, Russia. We used 12 chloroplast microsatellite loci (n = 935 individuals) and two chloroplast noncoding regions (rpl16 intron, petL‐psbE intergenic spacer; n = 33 individuals). The genetic diversity, genetic structure, phylogenetic relationships of the four species were analyzed, and their ancestral areas were reconstructed. The high genetic diversity of the Jeju island population of E. byunsanensis and Russian populations of E. stellata indicated these species’ northward and southward dispersal, respectively. The genetic structure analyses suggest that the populations in these four species have limited geographical structure, except for the Chinese E. stellata population (SCP). The phylogenetic analyses suggest that E. byunsanensis and E. pinnatifida are sister species and that Chinese SCP may not belong to E. stellata. The ancestral area reconstruction revealed that the most recent common ancestor of the four species existed in the current Chinese habitat of E. stellata. This study shows that E. byunsanensis and E. pinnatifida originated from a southern Eranthis species and speciated into their current forms near Jeju island and near western regions of Japan, respectively, during the Miocene. E. stellata may have dispersed southward on and near the Korean peninsula, though its specific origin remains unclear. Interestingly, the Chinese E. stellata population SCP suggests that the Chinese population might be most ancient among all the four Eranthis species. E. pungdoensis may have allopatrically speciated from E. byunsanensis during the Holocene. The Korean peninsula and the surrounding areas can be considered interesting regions which provide the opportunity to observe both northern‐ and southern‐sourced Eranthis species.     

Identification of species in the angiosperm family Apiaceae using DNA barcodes

Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The Consortium for the Barcode of Life (CBOL) Plant Working Group has recommended the combination of rbcL+matK as the core plant barcode. Recently, the China Plant BOL Group proposed that the nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a subset of this marker (ITS2), be incorporated alongside rbcL+matK into the core barcode for seed plants, particularly angiosperms. In this study, we assess the effectiveness of these four markers plus psbA‐trnH as Apiaceae barcodes. A total of 6032 sequences representing 1957 species in 385 diverse genera were sampled, of which 211 sequences from 50 individuals (representing seven species) were newly obtained. Of these five markers, ITS and ITS2 showed superior results in intra‐ and interspecific divergence and DNA barcoding gap assessments. For the matched data set (173 samples representing 45 species in five genera), the ITS locus had the highest identification efficiency (73.3%), yet ITS2 also performed relatively well with 66.7% identification efficiency. The identification efficiency increased to 82.2% when using an ITS+psbA‐trnH marker combination (ITS2+psbA‐trnH was 80%), which was significantly higher than that of rbcL+matK (40%). For the full sample data set (3052 ITS sequences, 3732 ITS2 sequences, 1011 psbA‐trnH sequences, 567 matK sequences and 566 rbcL sequences), ITS, ITS2, psbA‐trnH, matK and rbcL had 70.0%, 64.3%, 49.5%, 38.6% and 32.1% discrimination abilities, respectively. These results confirm that ITS or its subset ITS2 be incorporated into the core barcode for Apiaceae and that the combination of ITS/ITS2+psbA‐trnH has much potential value as a powerful, standard DNA barcode for Apiaceae identification.