How to fill the biodiversity data gap:Is it better to invest in fieldwork or curation?

Data gaps and biases are two important issues that affect the quality of biodiversity information and downstream results.Understanding how best to fill existing gaps and account for biases is necessary to improve our current information most effectively.Two current main approaches for obtaining and improving data include(1)curation of biological collections,and(2)fieldwork.However,the comparative effectiveness of these approaches in improving biodiversity data remains little explored.We used the Flora de Bogota project to study the magnitude of change in species richness,spatial coverage,and sample coverage of plant records based on curation versus fieldwork.The process of curation resulted in a decrease in species richness(synonym and error removal),but it significantly increased the number of records per species.Fieldwork contributed to a slight increase in species richness,via accumulation of new records.Additionally,curation led to increases in spatial coverage,species observed by locality,the number of plant records by species,and localities by species compared to fieldwork.Overall,curationwas more efficient in producing new information compared to fieldwork,mainly because of the large number of records available in herbaria.We recommend intensive curatorial work as the first step in increasing biodiversity data quality and quantity,to identify bias and gaps at the regional scale that can then be targeted with fieldwork.The stepwise strategy would enable fieldwork to be planned more costeffectively given the limited resources for biodiversity exploration and characterization.

Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea(Camellia sinensis var.assamica)

Chinese Assam tea(Camellia sinensis var.assamica)is an important tea crop with a long history of cultivation in Yunnan,China.Despite its potential value as a genetic resource,its genetic diversity and domestication/breeding history remain unclear.To address this issue,we genotyped 469 ancient tea plant trees representing 26 C.sinensis var.assamica populations,plus two of its wild relatives(six and three populations of C.taliensis and C.crassicolumna,respectively)using 16 nuclear microsatellite loci.Results showed that Chinese Assam tea has a relatively high,but comparatively lower gene diversity(H_(S)=0.638)than the wild relative C.crassicolumna(H_S=0.658).Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups,with considerable interspecific introgression.The Chinese Assam tea accessions clustered into three gene pools,corresponding well with their geographic distribution.However,New Hybrids analysis indicated that 68.48%of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools.In addition,10%of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C.taliensis.Our results suggest that Chinese Assam tea was domesticated separately in three gene pools(Puer,Lincang and Xishuangbanna)in the Mekong River valley and that the hybrids were subsequently selected during the domestication process.Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex,our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

Wind-dispersed seeds blur phylogeographic breaks:The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin

The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits.Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants.Here,we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa,a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China.We sequenced and analyzed three plastid DNA fragments(ptDNA) and eight nuclear microsatellites(nSSRs) of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range.Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa.This is consistent with the three phylogeographic breaks(Sichuan Basin,the Kaiyong Line and the 105°E line),where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups.However,the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks,and wind-dispersed seeds may be one of the main contributing factors.Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial.A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages.These results indicate that biological traits are likely to affect the evolutionary history of plants,and that nuclear molecular markers,which experience higher levels of gene flow,might be better indicators of phylogeographic breaks.

新版国际植物命名法规(维也纳法规)中的主要变化

出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规(Vienna Code),取代了圣路易斯法规(Saint Louis Code)而成为管理植物学(包括藻类学和真菌学)科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别。这些区别包括两版法规在起始日期、有效发表、合格发表、化石植物、多型真菌、拼写和附录诸方面的不同。

国际植物命名法规中的术语介绍

现今，国际上已普遍接受国际植物命名法规（Internationalcodeofbotanicalnomenclature）作为管理植物学（包括藻类学和真菌学）科学命名的规则。该规则由历届国际植物学大会的命名法分会会议修订，因而每六年出版一次修订版。最新版的维也纳法规（ViennaCode；McNeilleta1．，2006；中文版：张丽兵译，2007）取代了前一版的圣路易斯法规（SaintLouisCode，Greutereta1．，2000；中文版：朱光华译，2001）。

为《Flora of China》提供的伞形科新资料(英文)

在为编写《FloraofChina》伞形科而进行的修订工作中 ,提出了 1 1个新组合 ,即矮小丝瓣芹Acrone maminus (M .F .Watson)M .F .Watson&Z .H .Pan ,短柄丝瓣芹A .brevipedicellatumZ .H .Pan&M .F .Watson ,川西当归Angelicasinensisvar.wilsonii (H .Wolff)Z .H .Pan&M .F .Watson ,云南细裂芹Harry smithiafranchetii(M .Hiroe)M .L .Sheh ,钝叶独活Heracleumcandicansvar.obtusifolium (Wall.exDC .)F .T .Pu&M .F .Watson ,中华天胡荽Hydrocotylehookerissp .chinensis(DunnexR .H .Shan&S .L .Liou)M .F .Watson&M .L .Sheh ,普渡天胡荽H .hookerissp .handelii(H .Wolff)M .F .Watson&M .L .Sheh ,锐棱岩风Libanotisgrubovii (V .M .Vinogradova)M .L .Sheh&M .F .Watson ,美脉藁本Ligusticumlikiangense(H .Wolff)F .T .Pu&M .F .Watson和线叶藁本L .nematophyllum (Pimenov&Kljuykov)F .T .Pu&M .F .Watson ,无管藁本L .nullivittatum (K .T .Fu)F .T .Pu&M .F .Watson和二色棱子芹Pleurospermumbicolor(Franch .)C .NormanexZ .H .Pan&M .F .Watson .;发现了 1个新种 ,即短柄丝瓣芹。此外 ,还为Pleu rospermumgovanianumvar.bicolorFranch .指定了后选模式。

Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains

Elevation plays a crucial factor in the distribution of plants,as environmental conditions become increasingly harsh at higher elevations.Previous studies have mainly focused on the effects of large-scale elevational gradients on plants,with little attention on the impact of smaller-scale gradients.In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains.We found that the genetic structure(single,clonal,mosaic)of J.squamata shrubs is affected by differences in elevational gradients of only 150 m.Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower-or higher-elevation plots.Human activity can significantly affect genetic structure,as well as reproductive strategy and genetic diversity.Sub-populations at mid-elevations had the highest yield of seed cones,lower levels of asexual reproduction and higher levels of genetic diversity.This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations.Our findings provide new insights into the finer scale genetic structure of alpine shrubs,which may improve the conservation and management of shrublands,a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.

英国多克隐花植物保护区森林土壤和凋落叶特性及其与真菌的关系(英文)

报道了英国独特的真菌保护区里真菌的生态学和生物多样性,而该保护区内有关物种构成的数据自1994年就开始进行收集了。关于真菌的生态学相互关系以及它们在总的生态系统功能中的作用可以作为生物多样性数据的补充。5~8月期间,在8块覆盖着不同植被（山毛榉,桦树,桦栎山毛榉,禾本科植物）实验区里,研究了森林凋落叶和叶本层土壤的特性和构成,测量了细菌种群数量和真菌的生物量（针对麦角固醇而言）。用相关分析和分段回归建模方法,结合可通过并行研究采集到的原生动物和线虫数据,得到了一系列结果。这些结果强调了某些因素的复杂性,这些因素影响着森林土壤和森林凋落叶中真菌生物量空间可变性的时间动态。大多数的相互作用看起来是瞬时的,在解释环境观测记录时应该对这一点给予充分考虑。最后,解释了若干具体关系,给出了进一步研究的方向,讨论了对整个生态系统功能研究的必要性。

The many roles of small RNAs in leaf development

Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.

Bambusicolous fungi

Fourty-three species of microfungi from bamboo are treated,including one new family,Occultibambusaceae,three new genera,Neoanthostomella,Occultibambusa and Seriascoma,27 new species,one renamed species and 15 redescribed or re-illustrated species,and four designated reference specimens are treated in this paper,the majority of which are saprobic on dead culms.To determine species identification,separate phylogenetical analyses for each group are carried out,based on molecular data from this study and sequences downloaded from GenBank.Morphologically similar species and phylogenetically close taxa are compared and discussed.In addition a list of bambusicolous fungi published since Hyde and colleagues in 2002 is provided.

Microfungi on Tectona grandis(teak)in Northern Thailand

To date there is virtually no information available concerning the fungi associated with Tectona grandis(teak)(Lamiaceae)in Thailand.In this study,samples of microfungi were collected from both asymptomatic stems and dead wood,and symptomatic branches,stem and leaves of T.grandisfrom 27 sites in six provinces(Chiang Mai,Chiang Rai,Phayao,Phitsanulok,Phrae and Uttaradit Provinces).Morphology and combined multi-gene phylogeny(CAL,GAPDH,ITS,LSU,RPB2,SSU,TEF1 and TUB)were used to identify taxa.A total of 270 collections,representing 28 fungal species residing in 12 families,7 orders and 21 genera,with three species of uncertain taxonomic placement were identified.Of these,one family,three genera and 14 species are new to science.The new family,Pseudocoleodictyosporaceae is introduced based on its distinct lineage in the Dothideomycetes and its unique morphology as compared to Roussoellaceae and Torulaceae.The new genera are Neooccultibambusa,Pseudocoleodictyospora and Subglobosporium.The newly described species are Diaporthe neoraonikayaporum,D.tectonendophytica,D.tectonae,D.tectonigena,Hermatomyces tectonae,H.thailandica,Manoharachariella tectonae,Neooccultibambusa chiangraiensis,Pseudocoleodictyospora sukhothaiensis,Ps.tectonae,Ps.thailandica,Rhytidhysteron tectonae,Subglobosporium tectonae and Tubeufia tectonae.Fourteen species are known published taxa including Alternaria tillandsiae,Berkleasmium talaumae,Boerlagiomyces macrospora,Ceratocladium purpureogriseum,Fusarium solani,Helicoma siamense,Lasiodiplodia theobromae,Macrovalsaria megalospora,Paradictyoarthrinium diffractum,Phaeoacremonium italicum,Sphaeropsis eucalypticola,Stachybotrys levispora,St.renispora and Thaxteriellopsis lignicola.Epitypifications or reference specimens are designated for Boerlagiomyces macrospora and Macrovalsaria megalospora.Macrovalsaria megalospora is transferred from Botryosphaeriaceae to Dothideomycetes genus,incertae sedis based on taxonomy and phylogenetic analysis,which indicate it is distinct from Botryosphaeriaceae.All fungal species represent first reports on T.grandisin Thailand.New taxa and taxa incertae sedis,as well as known taxa which are established as reference specimens or epitypes,are presented with phylogenetic tree analyses,habitat,known distribution,material examined,full descriptions,notes and figures.Information is also provided for known taxa to add to the body of knowledge and to assist those wishing to study fungi occurring on T.grandis in future.

在墨尔本召开的第18届国际植物学大会做出的有关名称发表要求的变化——电子出版物对你意味着什么?

《国际植物命名法规》的修订由每六年一次的国际植物学大会(IBC)命名分会来决定。第18届国际植物学大会在澳大利亚墨尔本举行;命名分会于2011年7月18日至22日召开,其决议获得7月30日的全体会议通过。"墨尔本法规"有几个重要的变化,将影响新名称的发表。这些变化中的两个将在"墨尔本法规"出版前的几个月,即于2012年1月1日起生效。通过以移动文档格式(Portable Document Format;pdf)在线发表的具有国际标准连续出版物号(ISSN)或国际标准图书编号(ISBN)的电子出版物,将构成有效发表。新分类群名称的合格发表所必须的拉丁文描述或特征集要将更改为拉丁文或英文描述或特征集要。此外,自2013年1月1日起,被处理为真菌的生物的新名称必须在原始资料(某一名称合格发表时与之有关的所有资料)中引证一个由一家公认的存储库(例如MycoBank)签发的标识码,才构成合格发表。本文提供了有关电子出版物的新规则的草案文本,并概述了相应的最佳做法。

Phylogenetic insights resolve Dacampiaceae(Pleosporales)as polyphyletic:Didymocyrtis(Pleosporales,Phaeosphaeriaceae)with Phoma-like anamorphs resurrected and segregated from Polycoccum(Trypetheliales,Polycoccaceae fam.nov.)

A phylogenetic analysis of nuLSU and ITS sequences representing genera previously included in Dacampiaceae indicates that the family is strongly polyphyletic and that the type species of Dacampia is placed in Pleosporales.The genus Munkovalsaria s.str.is placed in Didymosphaeriaceae(Pleosporales).Polycoccum s.str.and two species of Clypeococcum are shown to form a new lineage sister to the Trypetheliaceae in Trypetheliales and described here as Polycoccaceae.Other members of Polycoccum s.lat.are included in the Pleosporales and are closely related to lichenicolous Phoma-like species of the family Phaeosphaeriaceae.The genus Didymocyrtis is resurrected for these species and for lichenicolous species previously assigned to Diederichia,Diederichomyces,Leptosphaeria and Phoma.The genera Diederichia and Diederichomyces are synonymized with Didymocyrtis.The new combinations Didymocyrtis bryonthae,D.cladoniicola,D.foliaceiphila,D.infestans,D.kaernefeltii,D.melanelixiae,D.pseudeverniae,D.ramalinae,D.slaptoniensis and D.xanthomendozae are made,and the new name D.epiphyscia is introduced for Phoma physciicola.Some anamorph-teleomorph relationships are resolved,such as Didymocyrtis ramalinae–Phoma ficuzzae and Didymocyrtis consimilis–Phoma caloplacae,the phylogenetic results being supported by single ascospore cultures that lead to the asexual stage producing pycnidia and conidia in culture.Speciation by host switching is assumed to be important in the genus Didymocyrtis.An identification key to Didymocyrtis species is provided.

Natural traps of spores and pollen grains from the region surrounding Wenbi Reservoir, Yunnan, China

We did a comparative analysis of pollen and spores from five kinds of natural pollen traps at Wenbi Reservoir, northwest Yunnan, China. The natural traps were the surface soil, ground inhabiting mosses, spider webs, tree bark and moss/lichen on trees. These traps showed qualitative and quantitative variations in the pollen and spore spectra. The palynomorphs recovered from the soil samples of trees and shrubs ranged from 90.54% to 95.98% of the total counts. These counts were higher than counts from ground mosses(53.13%–81.66%), spider webs(61.71%), bark samples(53.8%) and moss/lichen on trees(50%–53.6%). The result of pollen/spore analysis showed that surface soil, ground mosses and spider webs better reflect the local vegetation compared with tree bark or moss/lichen on trees.

Pollen Morphology of Eight Genera of the Subtribe Mutisiinae Less. sensu Bremer （Compositae） from Asia

The pollen morphology of 28 species and one variety representing eight genera of the subtribe Mutisiinae Less. sensu Bremer （Compositae） was investigated by scanning electron microscopy （SEM） and light microscopy. The pollen grains are usually radically symmetrical, isopolar, and tricolporate. The shape varies from spheroidal to subprolate in equatorial view and is three-lobed circular in polar view. Based on exine sculpturing observed under SEM, the pollen grains can be divided into three types： （i） type Ⅰ, with macrogranulate sculpture; （ii） type Ⅱ, with a finely granulate sculpture; and （iii） type Ⅲ with spiny sculpture. The palynological data showed that the Macroclinidium Maxim. was remarkably distinguished from those of the other seven genera. The variation of pollen characteristics within the Mutisiinae in Asia is little at species level, but it proves some useful information for studying the relationships among genera and it has an important significance in further understanding the evolutionary history of Mutisiinae.

Phylogenetic relationships and morphological reappraisal of Melanommataceae(Pleosporales)

The family Melanommataceae is widespread in temperate and subtropical regions and species invariably occur on twigs or bark of various woody plants in terrestrial,marine or freshwater habitats.In this paper,the type species of 26 genera of the family are re-described and illustrated.A multi-gene phylogeny based on maximum likelihood and Bayesian analyses of LSU,SSU,RPB2 and EF-1αsequence data of species of Melanommataceae is provided.The new genera,Muriformistrickeria,Pseudostrickeria and Thysanolaenae are introduced.Anomalemma is synonymized under Exosporiella.Acrocordiopsis,Astrosphaeriella,Beverwykella,Caryosporella,Sporidesmiella and Pseudotrichia are excluded from Melanommataceae based on molecular phylogenetic analyses.Presently,20 genera are accepted in Melanommataceae.Based on the phylogenetic data,five new species,Byssosphaeria siamensis,Herpotrichia vaginatispora,Pseudostrickeria muriformis,Pseudostrickeria ononidis and Muriformistrickeria rubi,are introduced.

Dictyosporiaceae fam.nov.

Dictyosporiaceae fam.nov.is introduced to accommodate a holomorphic group of Dothideomycetes that are saprobes on decaying wood and plant debris in terrestrial and freshwater habitats.The sexual morph comprises Dictyosporium meiosporum,D.sexualis,Gregarithecium curvisporum,Pseudocoleophoma calamagrostidis and P.polygonicola.The sexual morphs are characterized by immersed to erumpent,superficial,globose to subglobose,dark brown to black ascomata,bitunicate asci,and septate,hyaline,sheathed ascospores.The asexual morphs are hyphomycetous with brown,multi-septate,cheirosporous conidia,produced from holoblastic conidiogenous cells,on micronematous conidiophores.Phylogenetic analyses of LSU,SSU and TEF1 sequence data place the genera with cheirospores in a monophyletic clade in the order Pleosporales.Phylogenetic analyses based on ITS sequence data show the family to comprise 44 distinct lineages that correspond to ten genera and an undetermined genus.Four new genera Dictyocheirospora,Dictyopalmispora,Jalapriya and Vikalpa,and eight new species Dictyocheirospora bannica,D.rotunda,D.vinaya,Dictyopalmispora palmae,Dictyosporium olivaceosporum,D.sexualis,Jalapriya pulchra,and Vikalpa lignicola,are introduced in the family.

Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island

Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation.However,polyploid groups are understudied due to complex sequence homology,challenging genome assembly,and taxonomic complexity.Here,we study adaptive divergence in taxonomically complex eyebrights(Euphrasia),where recent divergence,phenotypic plasticity,and hybridization blur species boundaries.We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle,a small isolated island in the British Isles.Using a common garden experiment,we show a genetic component to the morphological differences present between these species.Using wholegenome sequencing and a novel k-mer approach we call“Tetmer”,we demonstrate that the species are of allopolyploid origin,with a sub-genome divergence of approximately 5%.Using2 million SNPs,we show sub-genome homology across species,with a very low sequence divergence characteristic of recent speciation.This genetic variation is broadly structured by species,with clear divergence of Fair Isle heathland Euphrasia micrantha,while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related.Overall,we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence,where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers(bitunicate asci)and often with fissitunicate dehiscence.Many species are saprobes,with many asexual states comprising important plant pathogens.They are also endophytes,epiphytes,fungicolous,lichenized,or lichenicolous fungi.They occur in terrestrial,freshwater and marine habitats in almost every part of the world.We accept 105 families in Dothideomycetes with the new families Anteagloniaceae,Bambusicolaceae,Biatriosporaceae,Lichenoconiaceae,Muyocopronaceae,Paranectriellaceae,Roussoellaceae,Salsugineaceae,Seynesiopeltidaceae and Thyridariaceae introduced in this paper.Each family is provided with a description and notes,including asexual and asexual states,and if more than one genus is included,the type genus is also characterized.Each family is provided with at least one figure-plate,usually illustrating the type genus,a list of accepted genera,including asexual genera,and a key to these genera.A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders,including the novel orders,Dyfrolomycetales,Lichenoconiales,Lichenotheliales,Monoblastiales,Natipusillales,Phaeotrichales and Strigulales.The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light.It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.