Phylogeny and Classification of Prunus sensu lato （Rosaceae）

The classification of the economically important genus Prunus L. sensu lato （s.L） is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.I. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions （atpB- rbcL, matK, ndhF, psbA-trnH, rbcL, rpL 16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycfl） and three nuclear genes （ITS, s6pdh and Sbel） to explore their infrageneric used to develop a new, phylogeny-based classification relationships. The results of these analyses were of Prunus s.I. Our phylogenetic reconstructions resolved three main clades of Prunus s.I. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades： subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae （T. T. yu ＆ L. T. Lu） S. L. Zhou and one new species name, Prunus tianshanica （Pojarkov） S. Shi, were proposed.     

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.     

Multilocus Phylogeny of Lycodon and the Taxonomic Revision of Oligodon multizonatum

Classification of the Asian snake genera Lycodon and Oligodon has proven challenging. We conducted a molecular phylogenetic analysis to estimate the phylogenetic relationships in the genus of Lycodon and clarify the taxonomic status of Oligodon multizonatum using mitochondrial（cyt b, ND4） and nuclear（c-mos） genes. Phylogenetic trees estimated using Maximum Likelihood and Bayesian Inference indicated that O. multizonatum is actually a species of Lycodon. Comparing morphological data from O. multizonatum and its closest relatives also supported this conclusion. Our results imply that a thorough review of the evolutionary relationships in the genus of Lycodon is strong suggested.     

Evidence for two types of Aquilegia ecalcarata and its implications for adaptation to new environmentsOA

Spurs have played an important role in the radiation of the genus Aquilegia,but little is known about how the spurless state arose in A.ecalcarata.Here we aim to characterize the genetic divergence within A.ecalcarata and gain insights into the origin of this species.A total of 19 populations from A.ecalcarata and 23 populations from three of its closest relatives(Aquilegia kansuensis,Aquilegia rockii and Aquilegia yabeana) were sampled in this study.We sequenced fifteen nuclear gene fragments a...     

Historical biogeography and evolutionary diversification of Lilium(Liliaceae): New insights from plastome phylogenomicsOA

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium(14plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a timecalibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic act...     

Systematic positions of Lamiophlomis and Paraphlomis （Lamiaceae） based on nuclear and chloroplast sequences

Genera Lamiophlomis and Paraphlomis were originally separated from genus Phlomis s.1. on the basis of particular morphological characteristics. However, their relationship was highly contentious, as evidenced by the literature. In the present paper, the systematic positions of Lamiophlomis, Paraphlomis, and their related genera were assessed based on nuclear internal transcribed spacer （ITS） and chloroplast rpl16 and trnL-F sequence data using maximum parsimony （MP） and Bayesian methods. and outgroup were sampled. Analyses of both separate In total, 24 species representing six genera of the ingroup and combined sequence data were conducted to resolve the systematic relationships of these genera. The results reveal that Lamiophlomis is nested within Phlomis sect. Phlomoides and its generic status is not supported. With the inclusion ofLamiophlomis rotata in sect. Phlomoides, sections Phlomis and Phlomoides of Phlomis were resolved as monophyletic. Paraphlomis was supported as an independent genus. However, the resolution of its monophyly conflicted between MP and Bayesian analyses, suggesting the need for expended sampling and further evidence.     

NSort/DB:An Intranuclear Compartment Protein Database

Distinct substructures within the nucleus are associated with a wide variety of important nuclear processes.Structures such as chromatin and nuclear pores have specific roles,while others such as Cajal bodies are more functionally varied.Understanding the roles of these membraneless intra-nuclear compartments requires extensive data sets covering nuclear and compartment-associated proteins.NSort/DB is a database providing access to intra-or sub-nuclear compartment associations for the mouse nuclear proteome.Based on resources ranging from large-scale curated data sets to detailed experiments,this data set provides a high-quality set of annotations of non-exclusive association of nuclear proteins with structures such as promyelocytic leukaemia bodies and chromatin.The database is searchable by protein identifier or compartment,and has a documented web service API.The search interface,web service and data download are all freely available online at http://www.nsort.org/db/.Availability of this data set will enable systematic analyses of the protein complements of nuclear compartments,improving our understanding of the diverse functional repertoire of these structures.     

Phylogeny,character evolution,and classification of Selaginellaceae(lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74% increase of the earlier largest sampling) representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylog...     

Analysis of plastid and nuclear DNA data in plant phylogenetics——evaluation and improvement

Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.     

Phylogenetics and biogeography of eastern Asian-North American disjunct genus Pachysandra （Buxaceae） inferred from nucleotide sequences

Pachysandra is an eastern Asian-North American disjtunct genus with three species, two in eastern Asia （Pachysandra axillaris and Pachysandra terminalis） and one in eastern North America （Pachysandra procurnbens）. Although morphological and cytological studies suggest a close affinity of Pprocumbens with P axillaris, molecular data from nuclear and chloroplast DNA regions have provided conflicting signals. In this study, we tested previous phylogenetic hypotheses using sequences of nuclear ribosomal DNA internal transcribed spacers and chloroplast ndhF gene from multiple individuals of each of the three species. We also estimated the time of divergence between eastem Asia and eastern North America. Our results support the morphological and cytological conclusion that P procumbens is more closely related to P axillaris than to P terminalis. The estimated time of divergence of P axillaris and P procumbens was 14.6±5.5 mya, consistent with estimates from many other eastern Asian-North American disjunct genera. The migration of Pachysandra populations from eastern Asia to North America might have occurred by way of the North Atlantic land bridge.     

Aphis （Hemiptera： Aphididae） species groups found in the Midwestern United States and their contribution to the phylogenetic knowledge of the genus

A phylogeny of the genus Aphis Linnaeus, 1 758 was built primarily from specimens collected in the Midwest of the United States. A data matrix was constructedwith 68 species and 41 morphological characters with respective character states of alate and apterous viviparous females. Dendrogram topologies of analyses performed usingUPGMA （Unweighted Pair Group Method with Arithmetic Mean）, Maximum Parsimony and Bayesian analysis of Cytochrome Oxidase I, Elongation Factor 1-α and primary endosymbiont Buchnera aphidicola 16S sequences were not congruent. Bayesian analysis strongly supported most terminal nodes of the phylogenetic trees. The phylogeny wasstrongly supported by EFI-α, and analysis of COl and EFI-α molecular data combined with morphological characters. It was not supported by single analysis of COI or Buch-hera aphidicola 16S. Results from the Bayesian phylogeny show 4 main species groups： asclepiadis,fabae, gossypii, and middletonii. Results place Aphis and species of the generaProtaphis Bōrner, 1952, Toxoptera Koch, 1856 and Xerobion Nevsky, 1928 in a monophyletic clade. Morphological characters support this monophyly as well. The phylogenyshows that the monophyletic clade of the North American middletonii species group belong to the genus Protaphis： P. debilicornis （Gillette ＆ Palmer, 1929）, comb. nov., P. echinaceae（Lagos and Voegtlin, 2009）, comb. nov., and P. middletonii （Thomas, 1879）. The genus Toxoptera should be considered a subgenus of Aphis （stat. nov.）. The analysis also indicatesthat the current genus Iowana Frison, 1954 should be considered a subgenus of Aphis （stat. nov.）.     

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...     

New patterns of the tree beta diversity and its determinants in the largest savanna and wetland biomes of South AmericaOA

Clear and data-driven bioregionalizations can provide a framework to test hypotheses and base biodiversity conservation.Here we used occurrence and abundance data in combination with objective analytical methods to propose two bioregionalization schemes for tree species of the Cerrado and the Pantanal in South America.We also evaluated the contribution of three sets of determinants of the occurrence-and abundance-based subregions.We compiled data on tree species composition from 894local assembl...     

Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus FargesiaOA

Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DN...     

Phylogeny of Ptychostomum （Bryaceae,Musci） inferred from sequences of nuclear ribosomal DNA internal transcribed spacer （ITS） and chloroplast rps4

The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.     

Pollen morphology of the genus Cornukaempferia （Zingiberaceae） in Thailand

Cornukaempferia is a recently described genus of Zingiberaceae which only occurs in Thailand as a rare genus with limited geographical distribution. Only three species have been described so far, including a recently described new species, C. larsenii. These three species are morphologically very similar and additional data on other biological aspects are useful for the elucidation of their relationship. Pollen morphology of all three species of genus Cornukaempferia has been studied by light microscopy and scanning electron microscopy. The pollen grains are monad, spherical, inaperturate. The exine sculpture is echinate with psilate between the spines for C. aurantiflora and C. longipetiolata, or echinate with regulate between the spines for C. larsenii. This observation helps support the taxonomic status of C. larsenii.     

A new genus of Asiatic short-tailed shrew(Soricidae,Eulipotyphla) based on molecular and morphological comparisons

Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist(mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies.However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages,one a close relative to B. quadraticauda, whereas the other—comprised of topotype specimens from southern Gansu—diverged from other Blarinella in the middle Miocene(ca. 18.2 million years ago(Ma),95% confidence interval=13.4–23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P~4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly,some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella.Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.     

中国鸡皮衣属二新记录种

1 INTRODUCTION Pertusaria is a fairly large genus of Pertusariaceae with around 170 species recognized(Kirk et al.2001).The genus is characterized by the verrucose thallus,and the large spores(often longer than 30μm)with a conspicuously thick wall(more than 2.5μm thick).Both morphology and chemistry are essential for identifying species in this genus(Oshio 1968; Dibben 1980; Archer 1991,1997;Lumbsch et al.1999).Studies of the Chinese Pertusaria have been extensively developed with 45taxa accepted to data(Zhao et al.2004).A considerable portion of these taxa are difficult to be distinguished without chemical data which,however,have been detected for only a handful of species (Yu et al.1999; Zhao et al.2004).     

Late Oligocene fossil acorns and nuts of Quercus section Cyclobalanopsis from the Nanning Basin,Guangxi,South ChinaOA

Quercus is the largest genus within the Fagaceae and has a rich fossil record.Most of the fossil material is attributed to the subgenus Quercus based on leaves,pollen or rarely acorns and nuts.Fossil records of Q.section Cyclobalanopsis characterized by ring-cupped acorns are relatively few and especially those described based on nuts are scant.In this study,we described four new species of Quercus section Cyclobalanopsis based on mummified acorns and nuts:Q.paleodisciformis X.Y.Liu et J.H.Jin s...