Molecular phylogeny and taxonomy of Phlomoides(Lamiaceae subfamily Lamioideae)in China:Insights from molecular and morphological data

Phlomoides,with 150-170 species,is the second largest and perhaps most taxonomically challenging genus within the subfamily Lamioideae(Lamiaceae).With about 60 species,China is one of three major biodiversity centers of Phlomoides.Although some Phlomoides species from China have been included in previous molecular phylogenetic studies,a robust and broad phylogeny of this lineage has yet to be completed.Moreover,given the myriad new additions to the genus,the existing infrageneric classification needs to be evaluated and revised.Here,we combine molecular and morphological data to investigate relationships within Phlomoides,with a focus on Chinese species.We observed that plastid DNA sequences can resolve relationships within Phlomoides better than nuclear ribosomal internal and external transcribed spacer regions(nrITS and nrETS).Molecular phylogenetic analyses confirm the monophyly of Phlomoides,but most previously defined infrageneric groups are not monophyletic.In addition,morphological analysis demonstrates the significant taxonomic value of eight characters to the genus.Based on our molecular phylogenetic analyses and morphological data,we establish a novel section Notochaete within Phlomoides,and propose three new combinations as well as three new synonyms.This study presents the first molecular phylogenetic analyses of Phlomoides in which taxa representative of the entire genus are included,and highlights the phylogenetic and taxonomic value of several morphological characters from species of Phlomoides from China.Our study suggests that a taxonomic revision and reclassification for the entire genus is necessary in the future.

Molecular Structure Tailoring of Organic Spacers for High‑Performance Ruddlesden–Popper Perovskite Solar Cells

Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(PSC)technology.However,two-dimensional(2D)or quasi-2D RP PSCs are encountered with some challenges of the large exciton binding energy,blocked charge transport and poor film quality,which restrict their photovoltaic performance.Fortunately,these issues can be readily resolved by rationally designing spacer cations of RPPs.This review mainly focuses on how to design the molecular structures of organic spacers and aims to endow RPPs with outstanding photovoltaic applications.We firstly elucidated the important roles of organic spacers in impacting crystallization kinetics,charge transporting ability and stability of RPPs.Then we brought three aspects to attention for designing organic spacers.Finally,we presented the specific molecular structure design strategies for organic spacers of RPPs aiming to improve photovoltaic performance of RP PSCs.These proposed strategies in this review will provide new avenues to develop novel organic spacers for RPPs and advance the development of RPP photovoltaic technology for future applications.

Decoding molecular mechanisms:brain aging and Alzheimer's disease

The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.

Molecular simulation study of the microstructures and properties of pyridinium ionic liquid[HPy][BF_(4)]mixed with acetonitrile

The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.

Molecular Phylogeny of the Lardizabalaceae Based on TrnL-F Sequences and Combined Chloroplast Data

The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and Takhtajan's tribal classification in both analyses. Decaisneae and Sinofranchetieae are basal clades in the phylogenetic trees and external to all other taxa in the family. Lardizabaleae consisting of Boquila and Lardizabala are well supported in both trn L_F (100%) analysis and trn L_F and rbc L combined analysis (99%). Tribe Akebieae are strongly supported by a bootstrap value of 100% in both trn L_F analysis and trn L_F and rbc L combined analysis. However, the new genus Archakebia is nested within the genus Akebia in the trn L_F trees. In the combined trees, Archakebia is sister to Akebia with high bootstrap support. The inter_relationships among three closely related genera Parvatia , Holboellia and Stauntonia are still problematic. P. brunoniana ssp. elliptica is sister to H. latifolia in both analyses with low bootstrap support. H. parviflora is nested within the Stauntonia and sister to S. cavalerieana . Therefore, these three genera of tribe Akebieae may not be monophylytic and their generic boundary and delimitation need to be further studied, by exploring more molecular data, together with more morphological characters.

Molecular Phylogeny of Bisexual Artemia Based on 16S rDNA

[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homologous sequences between them and 11 relative species of Artemia from GenBank were compared;the molecular phylogenetic tree was constructed by Mega Microsoft using Artemiopsis stefanssoni as outgroup.[Result] Artemia persimilis was the primal group in genus Artemia;Artemia franciscana and Artemia monica were the evolved groups;Artemia urmiana,Artemia sinica and other Artemia species from China shared a close genetic relationship.[Conclusion] Based on the 16S rDNA sequence of them,the phylogenetic relationships of these bisexual Artemia species were A.persimilis→A.urmiana,A.sinica and A.tibetiana→A.tunisiana→A.monica→A.Franciscan.

AdvancesinB0tryosphaeriaceae：identification，phylogenyandmolecularecology

葡萄座腔菌科（Botryosphaeriaceae）真菌是农业和林业上重要的病原菌、内生真菌或潜在的致病菌，主要引起树木溃疡病。这类真菌种类繁多，寄主范围广，广泛分布于全球，在生态系统中占有重要的地位。综述了近年来国内外在葡萄座腔菌科的分子生态学研究方面取得的新进展。介绍了葡萄座腔菌科真菌物种鉴定及其研究方法方面的发展，并列出了2006年以来发现的6个新属和38个新种；概述了该科各个种、属之间的系统发育关系以及科内区分的18个群。在真菌种群遗传结构及其与寄主关系方面，已有研究表明葡萄座腔菌科真菌大体可分为寄主专化型和广谱寄生型两种类型，并已经揭示了无性型为Diplodia，Lasiodiplodia和Dothiorella等部分种群的遗传结构及它们与寄主之间的联系。在种内遗传多样性和基因流动研究方面，展示了利用ISSR、SSR等分子标记方法取得的一些重要结果，有些种群（如Lasiodiplodia theobromae）没有寄主专化性，它们在不同寄主间表现出很强的基因流动，但在不同区域内的基因交流却很有限。讨论了该科分子生态学研究有待进一步解决的问题。

Molecular Phylogeny of the Higher Category of Acrididae (Orthoptera: Acridoidea)

The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as sample taxa. The sequence constitutions and variations were analyzed and the molecular phylogenetic trees were reconstructed based on the combined sequence data （795bp length in total） of 12S rDNA and 16S rDNA, using the grasshopper Pyrgomorpha conica of Pyrgomorphidae as the outgroup. The results showed that the rates of the two kinds of transitions are obviously much higher than that of the four kinds of Wansversions in these combined 12S＋16S rDNA sequence data. The saturation ofnucleotide substitutions happened in 12S and 16S rDNA sequence data. The molecular phylogenetic trees indicated that Oedipodinae is a monophyletic group and this subfamily is a natural one, but Catantopinae and Acridinae are non-monophyletic. Oedipodnae is a relatively primitive group within the Acrididae, whereas the Oxyinae may have diverged later than Oedipodinae, but earlier than most other species of Acridide.

Molecular Phylogeny and Phylogeography of Suidae

Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.

A Molecular Phylogeny of Macaca Based on Mitochondrial Control Region Sequences

Nucleotide sequences of segments of the mitochondrial control regions were analyzed to infer the phylogenetic relationships among 7 macaques.High nucleotide diversity in Macaca assamensis and relatively low diversity in M.thibetana were found.Based on the ML tree from control regions,species in our study can roughly be sorted into three species groups except for the phylogenetic position of M.fascicularis,i.e.,silenus group,including M.leonina;sinica group,including M.arctoides,M.assamensis,and M.thibetana;and fascicularis group,including M.mulatta and M.cyclopis.A discrepancy between earlier studies (Fooden & Lanyon,1989;Tosi et al,2003a;Deinard & Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales & Melnick,1998),our result supported the hypothesis that M.fascicularis diverged earlier than M.leonina.Mitochondrial paraphyly in eastern M.mulatta (with respect to M.cyclopis) and eastern M.assamensis (with respect to M.thibetana) were clearly observed in our study.In accordance with the results of Y chromosome,allozyme,nuclear genes and some morphological data (Delson,1980;Fooden & Lanyon,1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard & Smith,2001),our study on control region sequences supported M.arctoides to be classified into the sinica group.However,this result disagreed with the previous mtDNA studies (Hayasaka et al,1996;Morales & Melnick,1998;Tosi et al,2003a).

Molecular Phylogeny of Slow Lorises (Nycticebus) Revealed by D-loop Sequences and Complete Cytochrome b Gene Sequences of Mitochondrial DNA

Partial sequences of the D-loop and the complete sequences of cytochrome b gene (1 140 bp) of the slow lorises (genus Nycticebus) were undertaken to investigate evolutionary relationships among species of Nycticebus.Sequence analysis results consistently provide new taxonomy evidence at the DNA level for supporting Ratajszczak and Groves’ viewpoint that N.intermedus is merely the adult of N.pygmaeus (Ratajszczak,1998;Groves,1971).Phylogenetic analysis was performed by means of the combined data and these two separate sequences data,respectively,by using various methods,supporting the same topology,in which genus Nycticebus was formed of two clusters.The first cluster was composed of N.pygmaeus,and the second cluster of N.coucang.It also could provide a new molecular genetic evidence to support the view that the genus comprises two species:N.coucang and N.pygmaeus.

Morphology and molecular phylogeny of Paragorgia rubra sp.nov.(Cnidaria:Octocorallia),a new bubblegum coral species from a seamount in the tropical Western Pacific

A new species of bubblegum coral, Paragorgia rubra sp. nov., discovered from a seamount at a water depth of 373 m near the Yap Trench is studied using morphological and molecular approaches. Paragorgia rubra sp. nov. is the fourth species of the genus found in the tropical Western Pacific. The new gorgonian is red-colored, uniplanar, and measures approximately 530 mm high and 440 mm wide, with autozooids distributed only on one side of the colony. Paragorgia rubra sp. nov. is most similar to P. kaupeka Sainchez, 2005, but differs distinctly in the polyp ovals with large and compound protuberances （vs. small and simple conical protuberances） and the medullar spindles possessing simple conical protuberances （vs. compound protuberances）. Moreover, P. rubra sp. nov. differs from P. kaupeka in the smaller length/ width ratio of surface radiates （1.53 vs. 1.75 ）. The genetic distance of the mtMutS gene between P. rubra sp. nov. and P. kaupeka is 0.66%, while the intraspecific distances within Paragorgia Milne-Edwards ＆ Haime, 1857 except the species P. regalis complex are no more than 0.5%, further supporting the establishment of the new species. Furthermore, the ITS2 secondary structure ofP. rubra sp. nov. is also different from those of congeners. Phylogenetic analyses indicate Paragorgia rubra sp. nov. and P. kaupeka form a clade, which branched early within Paragorgia and diversified approximately 15 Mya.

Molecular phylogeny,biogeography and character evolution of the montane genus Incarvillea Juss.(Bignoniaceae)

The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau(QTP)fosters habitat fragmentation that drives morphological differentiation of mountain plant species.Consequently,determining phylogenetic relationships between plant subgenera using morphological characters is unreliable.Therefore,we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea.We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference(BI),maximum likelihood(ML)and maximum parsimony(MP)analyses using three molecular data sets(trnL-trnF sequences,nr ITS sequences,and a data set of combined sequences)derived from 81%of the total species of the genus Incarvillea.Within the genus-level phylogenetic framework,we examined the character evolution of 10 key morphological characters,and inferred the ancestral area and biogeographical history of the genus.Our analyses revealed that the genus Incarvillea is monophyletic and originated in Central Asia during mid-Oligocene ca.29.42 Ma.The earliest diverging lineages were subsequently split into theWestern Himalaya and Sino-Himalaya during the early Miocene ca.21.12 Ma.These lineages resulted in five re-circumscribed subgenera(Amphicome,Olgaea,Niedzwedzkia,Incarvillea,and Pteroscleris).Moreover,character mapping revealed the ancestral character states of the genus Incarvillea(e.g.,suffruticose habit,cylindrical capsule shape,subligneous capsule texture,absence of capsule wing,and loculicidal capsule dehiscence)that are retained at the earliest diverging ancestral nodes across the genus.Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies,thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.

Molecular phylogeny of Solms-laubachia(Brassicaceae) s.l.,based on multiple nuclear and plastid DNA sequences,and its biogeographic implications

The Hengduan Mountains region of south-west China is a noted biodiversity,hotspot, but the geographic origins and historical assembly of its rich endemic flora, including the sky-island species ofSolms-laubachia Muschl. （Brassicaceae）, have been little studied. Previous molecular studies on the phylogeny of Solms-laubachia showed it to be paraphyletic, leading to considerable expansion not only of its taxonomic limits, but also its geographic range, with the inclusion of taxa from outside the Hengduan region. However, these studies provided little resolution of interspecific relationships, preventing inferences about historical biogeography within the clade. In the present study, new sequence data from two nuclear genes （LEAFY and G3pdh） and two chloroplast intergenic spacers （petN-psbM and psbM-trnD） were combined with existing markers to increase phylogenetic signals. Phaeonychium villosum （Maxim.） Al-Shehbaz was found to be nested within Solms-laubachia s.l. In general, phylogenetic relationships appear to be a good predictor of geography, with the Hengduan Mountain endemics embedded in a paraphyletic grade of species from the western Himalayas and central Asia, but they also imply morphological homoplasy, lncongruence was detected between the nuclear and chloroplast gene trees, perhaps resulting from incomplete lineage sorting of ancestral polymorphisms. The crown age ofSolms-laubachia s.l. was estimated to be approximately 1.42-3.68 mya, using Bayesian relaxed molecular clock analysis. Historical biogeographic analysis using a parametric dispersalextinction-cladogenesis model inferred central Asia and the western Himalayas as most probable ancestral range of Solms-laubachia s.l., and estimated higher rates of eastward expansion than westward during the diversification of descendant lineages. In summary, our results suggest that Solms-laubachia s.l. originated during the Pliocene in central Asia, and subsequently migrated eastward into the Hengduan Mountains, colonizing sky-island, alpine scree-slope habitats that may have provided novel ecological opportunity and accelerated speciation, ultimately establishing this region as the present center of diversity of the genus.

Molecular phylogeny of the genus Clibanarius(Decapoda: Anomura: Diogenidae) based on mitochondrial and nuclear DNA sequences

Clibanarius , a genus of hermit crabs, is one of the most diverse genera within Diogenidae. However, studies on the phylogeny within Clibanarius is very limited. We reconstruct the molecular phylogeny of the genus Clibanarius based on two mitochondrial (16S rRNA and COI) and two nuclear protein-coding (NaK and PEPCK) genes using a multigene phylogenetic approach. Eleven selected Clibanarius species from the Indo-West Pacifi c are analyzed and the Bayesian and maximum likelihood analyses produced identical results in topology. Results suggest that C . rutilus and C . infraspinatus are more closely related to each other than to C . snelliusi , and C . striolatus shows a close relationship to C . longitarsus . The close association of C . merguiensis with C . englaucus and C . humilis is strongly supported by the divergence of C . virescens from them. Our phylogenetic results contradict the morphological classifi cation scheme proposed for Clibanarius and indicate that the relative length of dactyls and propodi is not phylogenetically signifi cant in Clibanarius . In addition, we speculate that the morphological characteristic of the median cleft of the telson might be phylogenetically important for Clibanarius .

Molecular epidemiology and phylogeny of Nipah virus infection:A mini review

Nipah virus(Ni V) is a member of the genus Henipavirus of the family Paramyxoviridae,characterized by high pathogenicity and endemic in South Asia.It is classified as a Biosafety Level-4(BSL-4) agent.The case-fatality varies from 40%-70% depending on the severity of the disease and on the availability of adequate healthcare facilities.At present no antiviral drugs are available for Ni V disease and the treatment is just supportive.Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus.This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries.Thirty phylogenetic studies have been published from 2000 to 2015 years,searching on pub-med using the key words ‘Nipah virus AND phylogeny' and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed,typing the key words ‘Nipah virus AND molecular epidemiology'.Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics,to study their origin and evolution and finally to act with effective preventive measure.

Molecular Phylogeny of Pamphagidae(Acridoidea,Orthoptera) from China Based on Mitochondrial Cytochrome Oxidase I Sequences

Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit I（cox1） gene sequences.Eleven species of Pamphagidae from 7 genera were sequenced to obtain mt DNA data,along with 2 species from the Gen Bank nucleotide database.The results of sequence comparisons showed the cox1 gene is 1 534 bp in length,including 326 varible sites and 211 parsimonious information sites.The percentage of A ＋T is 67.1% in the nucleotide sequences,showing a strong AT bias.Genetic distances among subfamilies are 0.08.Using Locusta migratoria as outgroup,the phylogenetic trees were reconstructed with NJ,MP,ML and Bayesian inferences,and the results showed that the clustering results were approximately identical to that of classical morphological classification.Thrinchinae and Pamphaginae were a monophyletic group,respectively.Two species of the genus Asiotmethis of Prionotropisinae did not get together with other species of Prionotropisinae,classification position of Asiotmethis should be further discussed by both genetic markers and morphological features.The current genus Filchnerella of Prionotropisinae was not a monophyletic group.

Molecular phylogeny and divergence time of Trachypithecus： with implications for the taxonomy of T. phayrei

The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of Z phayrei using multiple genes. Our results support a sister-relationship between Z p. phayrei and T p. shanicus. However, the mitochondrial CYT B gene supported T. p. crepuscula as a distinct species, but the nuclear PRMI gene suggested a closer relationship between T p. crepuscula and T p. phayrei. The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred, a fact that would benefit from re-examination using multiple unlinked nuclear genes.

Morphology and molecular phylogeny of two colepid species from China, Coleps amphacanthus Ehrenberg, 1833 and Levicoleps biwae jejuensis Chen et al., 2016 （Ciliophora, Prostomatida）

Two colepid ciliates, Coleps amphacanthus Ehrenberg, 1833 and Levicoleps biwae jejuensis Chen et al., 2016, were first recorded in China. Their living morphology, infraciliature and small subunit （SSU） rRNA gene sequences were determined using standard methods. The improved diagnosis of Coleps amphacanthus is as follows： cell size about 100x 50 pm in vivo, barrel-shaped; 22-28 ciliary rows each composed of about 14-21 monokinetids and two perioral dikinetids; 5-10 caudal cilia; and one terminal contractile vacuole. Levicoleps biwae jejuensis was also investigated, with an improved diagnosis given based on previous and present work. The phylogenetic analyses based on SSU rRNA gene sequences revealed that all Coleps species were grouped together, except for Coleps amphacanthus, which was grouped into a clade of the genus Levicoleps.

Molecular Phylogeny Determined Using Chloroplast DNA Inferred a New Phylogenetic Relationship of <i>Rorippa aquatica</i>(Eaton) EJ Palmer &Steyermark (Brassicaceae)—Lake Cress

North American lake cress, Rorippa aquatica (Eaton) EJ Palmer & Steyermark (Brassicaceae), is listed as an endangered or threatened species. Lake cress shows heterophyllic changes in leaf form in response to the surrounding environment. Therefore, this species has received considerable attention from ecological and morphological perspectives. However, its phylogenetic position and taxonomic status have long been a subject of debate. To analyze the phylogenetic relationship of lake cress, we investigated chloroplast DNA sequences from 17 plant species. The results of phylogenetic reconstruction performed using trnL intron, trnG (GCC)-trnM (CAU), and psbC-trnS (UGA) indicated that lake cress is a member of Rorippa. Moreover, we found that the chromosome number of lake cress is 2n = 30. This result indicated that lake cress might have originated from aneuploidy of triploid species or via intergeneric crossing. Taken together, our results suggest an affinity between lake cress and Rorippa at the molecular level, indicating that lake cress should be treated as Rorippa aquatica (Eaton) EJ Palmer & Steyermark.