Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions,thus limiting their ability to expand into novel environments.However,the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood.The Niviventer niviventer species complex(NNSC),consisting of highly abundant wild rats in Southeast Asia and China,offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related.In the present study,we combined ecological niche modeling with phylogenetic analysis,which suggested that sister species cannot be both widespread and dominant within the same geographical region.Moreover,by assessing heterozygosity,linkage disequilibrium decay,and Tajima's D analysis,we found that widespread species exhibited higher genetic diversity than narrow-range species.In addition,by exploring the“genomic islands of speciation”,we identified 13 genes in highly divergent regions that were shared by the two widespread species,distinguishing them from their narrow-range counterparts.Functional annotation analysis indicated that these genes are involved in nervous system development and regulation.The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Special Issue Introduction-The Whitefly Bemisia tabaci Species Complex and Begomoviruses:Research Progress and Future Prospects

The whitefly Bemisia tabaci species complex and the begomoviruses they transmit are devastating agricultural pests worldwide.With the rapid and further inva-sions by some members of the whitefly species complex into new regions,their impacts on human society are likely to increase in the years to come.

The Bemisia tabaci species complex： Additions from different parts of the world

Bemisia tabaci is one of the most threatening pests in many crops. We sequenced part of the mitochondrial cytochrome oxidase I gene from fifty whitefly populations collected in Indonesia, Thailand, India and China. Nineteen unique sequences （haplotypes） of the cytochrome oxidase I were identified in these populations. They were combined with sequences available in databases, resulting in a total of 407 haplotypes and analyzed together with nine outgroup accessions. A phylogenetic tree was calculated using the maximum likelihood method. The tree showed that all groups that were found in previous studies were also present in our study. Additionally, seven new groups were identified based on the new haplotypes. Most B. tabaci haplotypes grouped based on their geographical origin. Two groups were found to have a worldwide distribution. Our results indicate that our knowledge on the species complex around B. tabaci is still far from complete.

A New Species of Japalura (Squamata: Sauria:Agamidae) from Upper Lancang (Mekong) Valley of Eastern Tibet, China

A new species of the agamid genus Japalura is described based on 15 specimens from the upper Lancang（Mekong） Valley of eastern Tibet, PR China. Populations of the new species, Japalura vela sp. nov., were previously recognized as J. flaviceps. The new species is morphologically most similar to J. batangensis, J. micangshanensis, J. variegata, and J. zhaoermii, but is distinguished from the four species and all remaining congeners by the following combination of morphological characters： 1） small adult size（SVL 56–69 mm in males, 59–66 mm in females）; 2） ratio of tail TAL/SVL 1.85–2.06; 3） ratio of hind limb HLL/SVL 0.72–0.81; 4） T4 S 24 or 25; 5） concealed tympanum; 6） transverse gular fold present; 7） gular pouch present; 8） axillary fold present; 9） a pronounced, continuous, sail-like vertebral crest along length of body in males; 10） ground dorsal coloration black in males; 11） distinct gray transverse streaks on dorsal surface of head; 12） black radiated streaks around eyes; 13） distinct, black vermiculate stripes on ventral surface of head in both sexes; 14） a strongly jagged dorsolateral stripe from neck to base of tail on each side of vertebral crest in males; and 15） absence of gular spots in both sexes. General distribution patterns of the genus in the Hengduan Mountains region are also discussed.

Bufo gargarizans:What’s in a Name?

The taxonomic status of Bufo species in East Asia,particularly those closely related to B.gargarizans,has been controversial for over half a century,and recent molecular studies further fueled the dispute.Whether B.andrewsi,B.bankorensis,B.minshanicus,B.sachalinensis,B.tibetanus,and B.tuberculatus constitute valid species or are geographic or ecological variants of B.gargarizans is at the centre of the discussion.Most of these forms possess morphological diagnostic traits,but those differences are minimal and often inconsistent.Molecular data produced many contradictory patterns.Lack of clear diagnostic characters,different usage or definition of various names,mis-identified specimens,limited amount of data or samples,and frequent inter-specific hybridization may all have contributed to the current controversies.Some contradiction may also result from differences between similarity-based clustering and gene tree-based branching patterns.Nevertheless,a dominant allopatric differentiation pattern within this species complex is apparent,and several regional population groups have been identified.Some of the groups resemble old names(e.g.B.minshanicus,B.tibetanus),while others are new.These groups may represent geographic or ecological variants,incipient species,or valid species,and the current data do not warrant a convincing taxonomic revision.To move forward,a single study with comprehensive sampling and genomic data is needed to establish a solid framework,which will define naturally existing population clusters/lineages,and detect their levels of divergence and approximate geographic boundaries.Morphological and ecological examination will follow to understand their biology,determine their taxonomic status,and identify consistent diagnostic characters if necessary.

Colletotrichum species and complexes:geographic distribution,host range and conservation status

The taxonomy of the genus Colletotrichum has undergone tremendous changes over the last decade,with over 200 species being currently recognised and species complexes being informally used to cluster those species.Many of these species are important plant pathogens,some rather polyphagous and others host-specific,but several occur seldomly and some may in fact be ecologically endangered.Based mainly on literature from the past decade,in this work we review the occurrence,geographic distribution and host spectrum of currently recognised Colletotrichum species under phylogenetic,pathologi-cal/agronomic and ecological perspectives,providing a list arranged by Colletotrichum species and species complexes.A total of 257 species are listed and grouped into 15 species complexes.In this work we have recorded 1353 unique host species-Colletotrichum species association records from 720 hosts,with the Fabaceae as the family with higher number of hosts(52 host species)but with the Rosaceae as the family with the highest number of host species-Colletotrichum species association records(118 association records).According to occurrence data,88 species are common in nature,128 were considered as data deficient and 41 are threatened,some of which are likely extinct from nature and preserved only in cul-ture collections.Several species are relevant plant pathogens,in some cases geographically confined and thus of potential quarantine relevance.Based on the major changes that occurred on Colletotrichum taxonomy over the last decade,this work provides a comprehensive overview of occurrence data of Colletotrichum species,compiling host range and geographical distribution,with relevance for plant pathology and conservation mycology.The current taxonomic framework in Colle-totrichum is revealing numerous species but poses challenges to the employment of standard criteria for the evaluation of biological conservation of these fungi.We advocate that conservation mycology and taxonomy should find common routes simultaneously enabling the correct delimitation of species of Colletotrichum and the implementation of feasible criteria for the evaluation of conservation.The employment of new technologies,such whole genome sequencing(WGS),will help and support the description of new species and to gain a better understanding of the genetic bases of speciation processes.

Wilt of Acer negundo L.caused by Fusarium nirenbergiae in China

Boxelder maple(Acer negundo L.)is widely grown as ornamental trees in China.In 2017 in Pizhou,Jiangsu Province,China,the boxelder maple trees suffered from a disease which caused wilting and yellowing leaves,rotted roots,and discolored xylem.The disease broke out from July to August.Seven fungal isolates were obtained from symptomatic tissue and tested for pathogenicity.Isolate An7 was isolated at high frequency from the discolored vascular tissues,which caused the wilt disease on healthy 2-year-old seedlings after inoculation and eventually killed all the seedlings.We conducted molecular analysis for An7,including the partial sequences of the rDNA internal transcribed spacer,calmodulin,RNA polymerase II second largest subunit and the translation elongation factor 1-αand evaluation of the variously sized conidia,chlamydospores and conidiophores and cultural traits.The pathogen was identified as Fusarium nirenbergiae,a member of the Fusarium oxysporum species complex.To our knowledge,this is the first report of F.nirenbergiae causing wilt on A.negundo in China.

The genus Thelonectria(Nectriaceae,Hypocreales,Ascomycota)and closely related species with cylindrocarpon-like asexual states

The genus Thelonectria and closely related species with cylindrocarpon-like asexual states are a group of perithecial ascomycetes in the family Nectriaceae that occur as saprobes and in few cases as pathogens of hardwood trees,shrubs or other plants.Although a key component of forest ecosystems around the world,species relationships and distributions of these fungi are largely unknown.The objectives of this study were to:1)infer species rank phylogenetic relationships of the genus Thelonectria and closely related species with cylindrocarpon-like asexual states and test the monophyly of each of the groups studied;2)delimit taxa establishing taxon circumscriptions;3)resolve nomenclatural issues by identifying redundantly used names and synonyms;and 4)provide an updated outline to the genus,geographical distributions data and identification tools,specifically diagnostic keys and molecular data that can be used as molecular barcodes.The recovered consensus phylogeny resulted in a narrow circumscription of the genus Thelonectria,based on the type T.discophora,excluding one of the common species T.jungneri.According to the phylogenetic analyses,T.jungneri belongs in a segregate clade that should be recognized as a different genus.In the genus Thelonectria,a total of four new species and three new combinations are recognized.Additionally,three new genera,closely related to Thelonectria,are described to accommodate species displaying a morphological resemblance to those of Thelonectria:Cinnamomeonectria gen.nov.with C.cinnamomea as type species,Macronectria gen.nov.with M.jungneri as type species and including four additional newly described species,and Tumenectria gen.nov.with T.laetidisca as type species.

Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski’s scorpion(Scorpiones: Buthidae) in arid Asian inland

Reliable delimitation of venomous scorpions is not only consequential to toxicological studies but also instructive to conservation and exploration of these important medical resources.In the present study,we delimited species boundary for the the Przewalski’s scorpion from arid northwest China through a combined approach employing phylogenetic analysis,ecological niche modeling and morphological comparison.Our results indicate that the Przewalski’s scorpion represent an independent taxonomic unit and should be recognized as full species rank,Mesobuthus przewalskii stat.nov.This species and the Chinese scorpion M.martensii represent the eastern members of the M.caucasicus species group which manifests a trans-Central Asia distribution across the Tianshan Mountains range.We also discussed the likely geographic barrier and climatic boundary that demarcate distributional range of the the Przewalski’s scorpion.

What are the common anthracnose pathogens of tropical fruits?

t Species of Colletotrichum are associated with anthracnose of a wide range of host plants including cultivated and wild tropical fruits.The genetic and ecological diversity of species associated with wild fruits are poorly explored,as compared to those associated with pre and postharvest diseases of cultivated fruits.In the present study,isolates of Colletotrichum were obtained from commercially available cultivated fruits,wild fruits(from native trees in natural habitats)and a few herbaceous hosts collected in northern Thailand.These isolates were initially characterized based on analysis of complete sequences of nuclear ribosomal internal transcribed spacer(ITS),into the genetically defined species complexes of Colletotrichum gloeosporioides,C.acutatum,C.boninense and C.truncatum.The isolates were primarily identified in the C.gloeosporioides species complex,based on a strongly supported clade within the ITS gene tree and were further characterized using multi-gene phylogenetic analyses and morphology.Phylogenetic analyses of ITS,partial sequences of actin(ACT),calmodulin(CAL),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),glutamine synthetase(GS)andβtubulin(TUB2)genetic markers were performed individually and in combination.Colletotrichum gloeosporioides sensu stricto was identified from lime(Citrus aurantifolia)and rose apple(Syzygium samarangense).Colletotrichum fructicola was isolated from dragon fruit(Hylocerous undatus)and jujube(Ziziphus sp.).Colletotrichum endophytica was found only from an unknown wild fruit.We observed a considerable genetic and host diversity of species occurring on tropical fruits within the clade previously known as Colletotrichum siamense sensu lato.The clade consists of isolates identified as pre and postharvest pathogens on a wide range of fruits,including coffee(Coffea arabica),custard apple(Annona reticulata),Cerbera sp.,figs(Ficus racemosa)mango(Mangifera indica),neem(Azadirachta indica)and papaya(Carica papaya)and was the dominant group of species among most wild fruits studied.With the exception of one isolate from banana,which grouped in the C.siamense clade,all the other isolates were identified as Colletotrichum musae.A new species,Colletotrichum syzygicola,associated with Syzygium samarangense in Thailand,is introduced with descriptions and illustrations.This study highlights the need to re-assess the evolutionary relationships of Colletotrichum species occurring on cultivated and wild fruits with emphasis on their ecology and cryptic diversification including sampling at regional and global scales.