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DNA barcoding and cryptic new species confirmation of Chimonocalamus(Poaceae:Bambusoideae) 认领 引用
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作者 Yu-Xiao Zhang Ru-Li Zhang +2 位作者 Xin-Yu Du Gui-Liang Zhang De-Zhu Li 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第2期240-259,共20页
Chimonocalamus is distinguished by pachymorph rhizome,lower culm nodes with a ring of root thorns,and semelauctant inflorescence.However,species identification in this genus can be confused due to similar morphologica... Chimonocalamus is distinguished by pachymorph rhizome,lower culm nodes with a ring of root thorns,and semelauctant inflorescence.However,species identification in this genus can be confused due to similar morphological features and overlapped geographical distribution.To confirm the identities of Chimonocalamus species in China,plastome and nuclear ribosomal(nrDNA)of 49 accessions of 10 known species and three putative new species were newly retrieved by genome skimming.Distance-based and tree-based methods were conducted to analyze the species discrimination rate of six datasets.The Skmer method was also applied.The results indicated that Skmer analyses had the highest discriminatory power with nine species identified(69.23%).The plastome showed much higher discriminatory success rate than the combination of three standard plastid DNA barcodes,which performed worst among the six datasets.The three potentially new species of Chimonocalamus were confirmed by the plastome and nrDNA datasets,and Skmer analysis,together with morphological differences.Herein,we describe and illustrate the three species as new to science,that is,Chimonocalamus hekouensis Y.X.Zhang,Gui L.Zhang&D.Z.Li,Chimonocalamus hsuehiorum D.Z.Li&Y.X.Zhang,and Chimonocalamus shuangjiangensis D.Z.Li&Y.X.Zhang.Moreover,the Chimonocalamus fimbriatus complex was designated,calling for further investigation.Taken together,plastome and nrDNA could serve as effective super-barcodes for species discrimination of Chimonocalamus,playing important roles in recognition of cryptic new species,and Skmer analysis can be adopted in molecular identification.Our study provides an empirical case for molecular discrimination of bamboos and can be meaningful for other plant groups. 展开更多
关键词 Chimonocalamus cryptic species genome skimming Skmer super-barcode
Reprogramming the Metabolome of Centella asiatica (L.) Urban Callus: Profiling of Newly Synthesized Cryptic Anthocyanins Triggered by LED Light Exposure 认领 引用
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作者 Claude Y.Hamany Djande Paul A.Steenkamp Ian A.Dubery 《Phyton-International Journal of Experimental Botany》 SCIE 2025年第4期1269-1286,共18页
Centella asiatica L.,a medicinal herb,has attracted substantial interest in research as well as commercial domains due to its bioactive compounds which include the pentacyclic triterpenoid centellosides,and in additio... Centella asiatica L.,a medicinal herb,has attracted substantial interest in research as well as commercial domains due to its bioactive compounds which include the pentacyclic triterpenoid centellosides,and in addition,hydroxy.In addition,hydroxycinnamic acid conjugates as well as flavonoids.The latter is the major class of secondary plant metabolites and comprises various subclasses,including anthocyanidins.Anthocyanins are rarely reported in extracts from C.asiatica and differ structurally due to a flavylium(2-phenylchromenylium)ion that carries a positive charge at the oxygen atom of the C-ring of the basic flavonoid structure.Callus of C.asiatica was initiated and propagated on synthetic media and subjected to different light regimes.White callus resulted from white fluorescent illumination,while purple callus developed in response to white light emitting diode(LED)illumination.To profile the metabolites responsible for the intense purple coloration,methanolic extracts were prepared from the two cell lines.Total phenolic,flavonoid,and anthocyanin content were determined and indicated(i)very low levels of flavonoids and anthocyanins in white callus and(ii)that anthocyanins dominate the flavonoid content of the purple callus.Extracts were subjected to untargeted ultra-high-performance liquid chromatography coupled to high-definition mass spectrometry(UHPLC–MS)to profile newly synthesized anthocyanins.Metabolite annotation was based on accurate mass determination and characteristic fragmentation patterns.Here,the reprogramming of the metabolome of white C.asiatica callus due to LED illumination is reported and the profiles of cryptic anthocyanins as well as putative flavonoid and caffeoylquinic acid co-pigments in purple callus are described. 展开更多
关键词 Anthocyanins callus Centella asiatica cryptic flavonoids liquid chromatography mass spectrometry reprogramming
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Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree(Davidia involucrata) revealed by whole genome resequencing 认领 引用 被引量：9
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作者 Yumeng Ren Lushui Zhang +5 位作者 Xuchen Yang Hao Lin Yupeng Sang Landi Feng Jianquan Liu Minghui Kang 《Plant Diversity》 SCIE CAS CSCD 2024年第2期169-180,共12页
The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However... The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories. 展开更多
关键词 Davidia involucrata Cryptic lineage Hybridization Population genomics Positive evolution
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Phylogenetic analyses and chromosome counts reveal multiple cryptic species in Bupleurum commelynoideum(Apiaceae) 认领 引用 被引量：3
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作者 Xiang-Guang Ma Cai Zhao +2 位作者 Chang-Bao Wang Qian-Long Liang Xing-Jin He 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2015年第1期104-116,共13页
Bupleurum commelynoideum H.Boissieu is a perennial herb occurring throughout the Hengduan Mountains region.This species was found to have more than one chromosome number in our previous chromosomal study.For a better ... Bupleurum commelynoideum H.Boissieu is a perennial herb occurring throughout the Hengduan Mountains region.This species was found to have more than one chromosome number in our previous chromosomal study.For a better understanding of its intraspeciflc genetic differentiation and interspecific relationships with other Bupleurum members,phylogenetic relationships among 15 populations of B.commelynoideum and 22 other Bupleurum members were investigated using the nuclear ribosomal DNA internal transcribed spacer(ITS)region and three chloroplast DNA(cpDNA)fragments(trnL-F,rps16,and rp132-trnL).Both phylogenetic analyses of the ITS region and combined cpDNA data indicated that B.commelynoideum has more than one geographically delimited lineage.Among them,accessions from Shangri-La and other regions were considered as different cryptic species according to the unified species concept.Our analyses also revealed that a complex pattern of reticulate relationship exists in B.commelynoideum and its allied species.The chromosome numbers of four populations of B.commelynoideum and a closely related species B.rockii H.Wolff are reported.The results showed that the chromosome number of B.commelynoideum has abundant variations in both chromosome ploidy(2x;4x;6x)and basic chromosome number(x=5;x=6).Population DXS(x=6),which has the different basic chromosome number,should represent a different kind of cryptic speciation in B.commelynoideum.The karyological evidence,together with the molecular data,indicated that the existence of at least three cryptic species in B.commelynoideum.This kind of genetic differentiation without morphological divergence might be caused by stabilizing selection imposed by the extreme environmental conditions of the alpine area. 展开更多
关键词 Bupleurum cryptic species genetic differentiation Hengduan Mountains stabilizing selection.
DNA barcoding and molecular phylogeny of Dumasia(Fabaceae:Phaseoleae)reveals a cryptic lineage 认领 引用 被引量：3
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作者 Kai-Wen Jiang Rong Zhang +2 位作者 Zhong-Fu Zhang Bo Pan Bin Tian 《Plant Diversity》 SCIE CAS CSCD 2020年第5期376-385,共10页
Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we ev... Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we evaluated the ability of six DNA barcoding sequences,one nuclear(ITS)and five chloroplast regions(trnH-psbA,matK,rbcL,trnL-trnF,psbB-psbF),to efficiently identify Dumasia species.Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation.Most combined analyses including ITS showed good species resolution and identification efficiency.We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia.The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches,which may result from cryptic differentiation.Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species. 展开更多
关键词 Cryptic species DNA barcoding Dumasia Internal transcribed spacer(ITS) Plastid genome
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Phylogeography and Cryptic Species Diversity of Paramesotriton caudopunctatus Species Group(Salamandridae: Paramesotriton) in Guizhou, China 认领 引用 被引量：3
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作者 Tao LUO Huamei WEN +2 位作者 Kai GAO Jun ZHOU Jiang ZHOU 《Asian Herpetological Research》 SCIE CSCD 2021年第2期188-200,共13页
The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary rel... The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal. 展开更多
关键词 P.caudopunctatus species group phylogeography cryptic diversity biogeography species delimitation Guizhou
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Distyly and cryptic heteromorphic self-incompatibility in A4ussaenda macrophylla (Rubiaceae) 认领 引用 被引量：3
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作者 Xiao-Qin Wu Pei-Xing Li +1 位作者 Xiao-Fang Deng Dian-Xiang Zhang 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2015年第2期166-178,共13页
Typical distylous species display both reciprocal herkogamy and heteromorphic incompatibility, which exclude self- and intramorph pollination and accordingly promote intermorph pollination. Here we explore an unusual ... Typical distylous species display both reciprocal herkogamy and heteromorphic incompatibility, which exclude self- and intramorph pollination and accordingly promote intermorph pollination. Here we explore an unusual distylous flower associated with self- and intramorph compatibility in Mussaenda macrophylla Wall. The species did not exhibit a precise reciprocal herkogamy, and the populations studied had a slight bias in favor of the short-styled morph （S-morph）. In addition, pollen tube growth in intermorph pollination was faster than either in intramorph or self-pollination, indicating that cryptic heteromorphic self-incompatibility occurred in M. macrophylla. Specifically, pollen tube growth rates after legitimate and illegitimate pollination were much more highly differentiated in long-styled morph （L-morph） than in S-morph, which might be attributed to the increased de- esterified pectin in the tip of L-morph pollen tube wall in comparison with S-morph. Transmission electron microscopic observation revealed illegitimate self-pollinated pollen tubes of two morphs were seriously degraded with the large autolysosome-like vacuoles in cytoplasm of L-morph pollen tube but accumulating small vacuoles in that of S-morph pollen tube, suggesting that incompatible pollen tubes might undergo autophagic programmed cell death except self-incompatible S-morph pollen tubes. Our results indicate that M. macrophylla is morphologically distylous with a cryptic heteromorphic self-incompatibility breeding system, which functions differently in S-morph with self-pollination compared with other illegitimate pollination. 展开更多
关键词 cryptic self-incompatibility distyly, Mussaenda macrophylla pollen tube growth, Rubiaceae.
The Effects of Space Dimension and Temperature on the Cross Mating of Three Cryptic Species of the Bemisia tabaci Complex in China 认领 引用 被引量：2
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作者 LI Xiao-xi LI Shao-jian +4 位作者 XUE Xia Muhammad Z Ahmed REN Shun-xiang Andrew G S Cuthbertson QIU Bao-li 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2012年第2期197-205,共9页
The sweetpotato whitefly Bemisia tabaci（Homoptera：Aleyrodidae）is a destructive pest of agriculture and horticulture worldwide.Recent phylogenetic analysis using mitochondrial cytochrome oxidase 1 sequences indicate... The sweetpotato whitefly Bemisia tabaci（Homoptera：Aleyrodidae）is a destructive pest of agriculture and horticulture worldwide.Recent phylogenetic analysis using mitochondrial cytochrome oxidase 1 sequences indicates that this whitefly is a species complex including at least 24 morphologically indistinguishable but genetically distinct cryptic species.In this study,the inter-species crosses of Middle East-Asia Minor 1（MEAM1）,Mediterranean（MED）and Asia II 7 cryptic species,which were referred to as B,Q and Cv biotypes before,were conducted in two different devices,leaf cages（7 cm3）and cylinder cages（280 cm3）,and at three temperatures of 22,30 and 38°C.Results indicated that no female progeny were produced in the reciprocal cross between MEAM1×Asia II 7,between MED×Asia II 7 cryptic species neither in leaf cage nor in cylinder cages,while 0.81 and 1.37% of females in the offspring were recorded in the reciprocal cross between MEAM1×MED in leaf cage experiments.Approximately 0.95-0.98% female progeny were recorded in the reciprocal cross between MEAM1×MED at 30°C,0.77% female progeny were recorded in the single cross direction between MEAM1 × MED at 22°C,and no female progeny were found in their reciprocal cross at 38°C in leaf cage.Our findings indicated that neither space dimension nor temperature have a significant effect on the hybridization of different B.tabaci cryptic species. 展开更多
关键词 Bemisia tabaci cross mating cryptic species reproductive isolation space dimension temperature
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Mitogenomic phylogeny,biogeography,and cryptic divergence of the genus Silurus(Siluriformes:Siluridae) 认领 引用 被引量：2
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作者 Weitao Chen Nicolas Hubert +11 位作者 Yuefei Li Shuli Zhu Jun Wang Denggao Xiang Shang Gao Chunni Kou Jilong Wang Tai Wang Zhiqiang Liang Junjie Wu Xinhui Li Jie Li 《Zoological Research》 SCIE CSCD 2024年第4期711-723,共13页
The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scie... The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scientific interest.Despite this interest,the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus.Herein,we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes(mitogenomes)from 13 morphological species to reconstruct the phylogenetic relationships,biogeographic history,and species diversity of Silurus.Our phylogenetic reconstructions identified eight clades,supported by both maximum-likelihood and Bayesian inference.Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units(MOTUs)in several taxa,including the Silurus asotus complex(four MOTUs)and Silurus microdorsalis(two MOTUs),suggesting that species diversity is underestimated in the genus.A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago(Ma),with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma,and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma.Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula,with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma.Key factors such as the Eocene-Oligocene extinction event,onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus. 展开更多
关键词 Maximum likelihood Bayesian inferences Ancestral area estimation Cryptic diversity Dispersal pathways Mitogenomes Sea levels
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DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the IndoWest Pacific oceans based on COI and 16S rRNA genes 认领 引用 被引量：1
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作者 WU Renxie ZHANG Haoran +3 位作者 LIU Jing NIU Sufang XIAO Yao CHEN Yongxia 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2018年第5期1753-1770,共18页
Sparids are of considerable economic importance in marine fishery and aquaculture in China, and the species diversity of this group is considered relatively high. However, the accurate species identification and delim... Sparids are of considerable economic importance in marine fishery and aquaculture in China, and the species diversity of this group is considered relatively high. However, the accurate species identification and delimitation of sparids in China remain unaddressed. In this study, we used mitochondrial cytochrome oxidase subunit ?(COI) and 16S ribosomal RNA(16S) genes to conduct DNA barcoding and species delimitation in eleven sparid species from the coastal waters of China. Based on Kimura-2 parameter genetic distances, the mean intraspecific/interspecific variation for COI and 16S were calculated as 0.004/0.152 and 0.002/0.072, respectively. All the conspecific individuals formed monophyletic clusters in neighbour-joining trees of both markers. An obvious barcoding gap was detected for each species, and a common genetic threshold of 1.3% sequence divergence was defined for species delimitation in both markers. Although the sequence variation of 16S was generally lower than that of COI, the results indicated that sparid species could be ef fectively and accurately identified and delimited by COI as well as 16S. Thus, we propose that the COI gene serve as the standard DNA barcode for sparids, and that the 16S gene could also be an ideal candidate barcode. Moreover, each of the six sparid species( Argyrops spinifer, Rhabdosargus sarba, Dentex hypselosomus, Acanthopagrus latus, Acanthopagrus australis and Acanthopagrus berda) showed high intraspecific divergence(>1.3% genetic threshold) with the remarkable geographic lineages in the Indo-West Pacific oceans, which supported that potential unrecognized cryptic species were in them. The potential cryptic diversity revealed here might be primarily attributed to the allopatric divergences caused by the long-term geographic isolation between the Indian and West Pacific oceans or between the opposite sides of the Indian Ocean. The results further suggest that a revision of taxonomic status of these species is required, followed by development of a biodiversity conservation strategy. 展开更多
关键词 SpaJcidae DNA barcoding species delimitation cryptic species Chinese coast Indo-West Pacific
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Integrative taxonomy recognized a new cryptic species within Stipa grandis from Loess Plateau of China 认领 引用 被引量：1
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作者 Bao Nie Bo-Han Jiao +3 位作者 Li-Fei Ren Polina D.Gudkova Wen-Li Chen Wen-Hao Zhang 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2022年第4期901-913,共13页
Stipa shanxiensis,a cryptic species within Stipa grandis that originated from central and western China,is described based on morphological,genomic,and ecological data from field and common garden experiments.Stipa sh... Stipa shanxiensis,a cryptic species within Stipa grandis that originated from central and western China,is described based on morphological,genomic,and ecological data from field and common garden experiments.Stipa shanxiensis morphologically resembles S.grandis,although phylogenetically it is closely related to the less morphologically similar Stipa baicalensis and Stipa krylovii.Of the eight significant morphological differences between S.shanxiensis and S.grandis,the two,cauline ligules longer than 2 cm with a filiform apex,and hairs shorter than 0.2 mm on the adaxial surface of the cauline uppermost leaves can be used to distinguish the species.Results from a common garden experiment verified that the two diagnostic characteristics were relatively stable and less morphologically plastic in response to environmental variation.Furthermore,a significant ecological divergence was found between S.shanxiensis and S.grandis,such that the former preferred warmer and more humid climates,and their predicted distribution was generally separated.Taken together,our results highlight that the integrative taxonomic approach was valuable for recognizing a new cryptic species in Stipa.In particular,we find that common garden experiments involving the effects of growth stage and characteristic position helped to morphologically diagnose cryptic species.These findings may also facilitate our understandings of ecological adaption and phenotypic plasticity in response to environmental change. 展开更多
关键词 common garden experiment cryptic species ecological divergence phenotypic plasticity Stipa
DNA reveals long-distance partial migratory behavior in a cryptic owl lineage 认领 引用 被引量：3
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作者 Keren R.Sadanandan David J.X.Tan +2 位作者 Kolbjorn Schjolberg Philip D.Round Frank E.Rheindt 《Chinese Birds》 CSCD 2015年第4期235-241,共7页
Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate mig... Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate migratory lineage Ninox japonica japonica and a mitochondrially distinct lineage of taxonomically uncertain status that has been recorded year-round at least in Taiwan.Overlap in ranges during migration and morphological similarity have led to difficulties in distinguishing the Brown Boobook from the Northern Boobook.Methods: PCR of cytochrome-b and Sanger sequencing of Ninox samples from Singapore and Brunei were used to determine sample identity.Results: Two out of four Singaporean samples and the Brunei sample were identified as Northern Boobooks.This is the first official record of this species in Singapore and represents a considerable range extension for the species.Further,the samples belong to the mitochondrially distinct lineage previously characterized in resident Taiwan Residents populations rather than to the well-known nominate migratory lineage.Conclusions: Our data show that the mitochondrial signature previously documented in resident Taiwan Residents populations of the Northern Boobook extends to migratory populations.This cryptic lineage may be more widespread in its breeding quarters,extending to the Chinese and Russian mainland,in which case the name florensis would apply to it.Further genetic and bioacoustic investigation is required to resolve the taxonomic status of this lineage. 展开更多
关键词 Migration Cryptic species Mitochondrial lineage Brown hawk owl Partial migrant
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Black-spotted pond frog (Pelophylax nigromaculatus) on the Chinese Loess Plateau represents a cryptic species: Evidence from molecular phylogeny and ecological niche modeling 认领 引用 被引量：1
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作者 De Ma Hua-Tao Liu +3 位作者 Ya-Jie Ji Cheng-Min Shi Yu-Hui Yang De-Xing Zhang 《Journal of Systematics and Evolution》 SCIE CAS CSCD 2015年第4期339-350,共12页
The black-spotted pond frog Pelophylax nigromaculatus is a typical temperate-adapted amphibian species, largely endemic to East Asia. It occurs from central, east, and northeast China, to the Russian Far East, the Kor... The black-spotted pond frog Pelophylax nigromaculatus is a typical temperate-adapted amphibian species, largely endemic to East Asia. It occurs from central, east, and northeast China, to the Russian Far East, the Korean Peninsula, and part of Japan. So far, little is known about this frog from the Loess Plateau, a region that has experienced profound changes in climate and environment since the late Miocene. Particularly, between the Loess Plateau and the North China Plain, stand the Luliang and Taihang mountain ranges, which form an important geographical divide in East China. Therefore, frogs from the Loess Plateau are indispensable for understanding the biogeography and evolution of this species. In this study, a total of 933 specimens of P. nigromaculatus collected range- wide were sequenced for the mitochondrial Cyt b gene, with 345 of them being genotyped at Io nuclear microsatellite loci. Both mitochondrial and microsatellite data resolved four major frog clades： （i） Loess Plateau clade, containing only frogs from the Loess Plateau; （ii） East China clade, containing frogs from the rest of China except those from the Liaodong Peninsula; （iii） Peninsulas clade, comprising frogs from the Korean Peninsula and Liaodong Peninsula; and （iv） Japan clade. Frogs from the Loess Plateau have deeply diverged from frogs in the remaining regions, with 11.5%- 13.1% sequence divergence, which is comparable to distances between congeneric ranid species. Ecological niche modeling analysis showed that the potential distribution ranges of the Loess Plateau frogs and the non-Loess Plateau frogs are rather different; niche identity testing indicated that the environmental niches of frogs from the Loess Plateau and other regions are not equivalent. Our data thus suggest that the Loess Plateau frogs represent a cryptic species. The uplift of the Luliang Mountains was the most plausible trigger of this cryptic diversification. 展开更多
关键词 cryptic species~ Korean Peninsula Liaodong Peninsula Loess Plateau pond frog Luliang Mountains Rananigromaculatus species delimitation.
Phylogenetic analysis reveals cryptic species diversity within minute intestinal fluke,Stellantchasmus falcatus Onji and Nishio,1916(Trematoda,Heterophyidae) 认领 引用 被引量：1
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作者 Chalobol Wongsawad Nattawadee Nantarat Pheravut Wongsawad 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2017年第2期159-163,共5页
Objective:To examine the taxonomic boundaries in the Stellantchasmus populations in different hosts and reveal the cryptic speciation of the Stellantchasmus in Thailand based on both morphological and molecular approa... Objective:To examine the taxonomic boundaries in the Stellantchasmus populations in different hosts and reveal the cryptic speciation of the Stellantchasmus in Thailand based on both morphological and molecular approaches.Methods:Stellantchasmus falcatus(S.falcatus) s.l.was collected from different hosts throughout Thailand.The worms were examined and measured.The nuclear ITS2 gene and the mitochondrial COI gene were used to investigate the S.falcatus s.l.from Dermogenus pusillus and Liza subviridis.Results:Stellantchasmus was one of food-borne trematode that widely distribute throughout Thailand.The comparison of S.falcatus s.l.from Dermogenus pusillus and Liza subviridis indicated a genetic divergence of nuD NA with 3.6% and mtD NA with 19.3%,respectively.Morphological characteristics were fairly different in the ratio of body size,length of prepharynx,and ratio of organ size.Conclusions:Our results provide initial evidence that S.falcatus s.l.from different hosts tend to be a different species based on both molecular and morphological characters.Cryptic species complexes are generally found among parasites that tend to have large populations and/or rapid evolution.The degree of genetic diversity existing would suggest the practice of targeted regimes to design and minimize these lections of anthelmintic resistance in the future. 展开更多
关键词 Cryptic species Trematode Host-parasite relationship Speciation Stellantchasmus
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Unraveling the cryptic Bemisia tabaci species complex:Global phylogenomic analysis reveals evolutionary relationships and biogeographic patterns 认领 引用
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作者 Hualing Wang Shilong Geng +19 位作者 Shusheng Liu Zhongtao Li Stephen Cameron Teng Lei Wei Xu Qing Liu Shuang Zuo Christopher A.Omongo M.N.Maruthi Habibu Mugerwa Xiaowei Wang Yinquan Liu Jesús Navas-Castillo Elvira Fiallo-Olivé Kyeong-Yeoll Lee Renate Krause-Sakate Hélène Delatte James Ng Susan Sea John Colvin 《Insect Science》 SCIE CAS CSCD 2026年第1期418-440,共23页
Bemisia tabaci is a complex of cryptic agro-economically important pest species characterized by diverse clades,substantial genetic diversity along with strong phylogeographic associations.However,a comprehensive phyl... Bemisia tabaci is a complex of cryptic agro-economically important pest species characterized by diverse clades,substantial genetic diversity along with strong phylogeographic associations.However,a comprehensive phylogenomic analysis across the entire complex has been lacking,we thus conducted phylogenomic analyses and explored biogeographic patterns using 680 single-copy nuclear genes(SCNs)obtained from whole-genome sequencing data of 58 globally sourced B.tabaci specimens.We constructed both concatenation and coalescent trees using 680 SCNs,which produced highly supported bootstrap values and nearly identical topologies for all major clades.When comparing these concatenation trees with those constructed using mitochondrial cytochrome oxidase I(mtCOI)and mitochondrial genome,we found conflicting phylogenetic relationships,with the later trees recovering fewer major clades.In a separate comparison between concatenation and coalescent trees,particularly those generated using IQ-TREE,they were found to delineate population relationships more effectively than RaxML.In contrast,coalescent phylogenies were proficient in elucidating geographical dispersal patterns and the reorganization of biological species.Furthermore,we provided a strict consensus tree that clearly defines relationships within most clades,laying a solid foundation for future research on the evolution and taxonomy of B.tabaci.Ancestral range estimates suggested that the ancestral region of the complex is likely situated in equatorial Africa,the Middle East,and Mediterranean regions.Subsequently,the expansion occurred into part of the Palearctic and further into the Nearctic,Neotropical,Indomalayan,and Australasian regions.These findings challenge both previous classifications and origin hypotheses,offering a notably more comprehensive understanding of the global distribution,evolutionary history,diversification,and biogeography of B.tabaci. 展开更多
关键词 ancestral geographic ranges Bemisia tabaci cryptic species phylogenomic tree species tree
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The cryptic lncRNA-encoded microprotein TPM3P9 drives oncogenic RNA splicing and tumorigenesis 认领 引用 被引量：3
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作者 Kun Meng Yuying Li +11 位作者 Xiaoyi Yuan Hui-Min Shen Li-Ling Hu Danya Liu Fujin Shi Dandan Zheng Xinyu Shi Nengqiao Wen Yun Cao Yun-Long Pan Qing-Yu He Chris Zhiyi Zhang 《Signal Transduction and Targeted Therapy》 SCIE CSCD 2025年第2期1069-1085,共17页
Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these micro... Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these microproteins in alternative splicing-driven tumor progression have rarely been studied.Here,we show that the novel protein TPM3P9,encoded by the lncRNA tropomyosin 3 pseudogene 9,exhibits oncogenic activity in clear cell renal cell carcinoma(ccRCC)by enhancing oncogenic RNA splicing.Overexpression of TPM3P9 promotes cell proliferation and tumor growth.Mechanistically,TPM3P9 binds to the RRM1 domain of the splicing factor RBM4 to inhibit RBM4-mediated exon skipping in the transcription factor TCF7L2.This results in increased expression of the oncogenic splice variant TCF7L2-L,which activates NF-κB signaling via its interaction with SAM68 to transcriptionally induce RELB expression.From a clinical perspective,TPM3P9 expression is upregulated in cancer tissues and is significantly correlated with the expression of TCF7L2-L and RELB.High TPM3P9 expression or low RBM4 expression is associated with poor survival in patients with ccRCC.Collectively,our findings functionally and clinically characterize the“noncoding RNA”-derived microprotein TPM3P9 and thus identify potential prognostic and therapeutic factors in renal cancer. 展开更多
关键词 tumorigenesis enhancing oncogenic rna splicingoverexpression lncrna tropomyosin cryptic lncrna encoded microprotein clear cell renal cell carcinoma ccrcc oncogenic rna splicing cryptic translation alternative splicing
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A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex,a global pest-species group 认领 引用 被引量：4
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作者 Hua-Ling Wang Teng Lei +14 位作者 Xiao-Wei Wang Stephen Cameron Jesús Navas-Castillo Yin-Quan Liu M.N.Maruthi Christopher A.Omongo Hélène Delatte Kyeong-Yeoll Lee Renate Krause-Sakate James Ng Susan Seal Elvira Fiallo-Olivé Kathryn Bushley John Colvin Shu-Sheng Liu 《Insect Science》 SCIE CAS CSCD 2025年第1期321-342,共22页
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities.Bemisia tabaci is a cryptic species complex containing more than 44 putative species;sever... Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities.Bemisia tabaci is a cryptic species complex containing more than 44 putative species;several of which are currently among the world's most destructive crop pests.Interpreting and delimiting the evolution of this species complex has proved problematic.To develop a comprehensive framework for species delimitation and identification,we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B.tabaci species complex acquired worldwide.Distinct datasets include full mitogenomes,single-copy nuclear genes,restriction site-associated DNA sequencing,geographic range,host speciation,and reproductive compatibility datasets.Phylogenetically,our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B.tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B.tabaci species diversity.Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples.Native geographic range information provides a complementary assessment of species recognition,while the host range datasets provide low rate of delimiting resolution.We further summarized different data performances in species classification when compared with reproductive compatibility,indicating that combination of mtCOI divergence,nuclear markers,geographic range provide a complementary assessment of species recognition.Finally,we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles. 展开更多
关键词 Bemisia tabaci cryptic species phylogenetics RAD-Seq reproductive compatibility whiteflies
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Unveiling Cryptic Diversity in Hylomys:A Commentary on Recent Taxonomic Revisions 认领 引用
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作者 Kai He Ying Zeng +12 位作者 Xing Chen Weipeng Bai Hongzhou Lin Jianhai Chen Nedko Nedyalkov Nobuyuki Yamaguchi Keerthy Vijayan Ramamoorthy Suganthasakthivel Brawin Kumar Yuqing Han Zhongzheng Chen Wenzhi Wang Yang Liu 《Integrative Zoology》 SCIE CAS CSCD 2025年第5期1087-1089,共3页
In Zeng et al.(2024),we employed mitochondrial genome sequencing to investigate the evolutionary history and cryptic diversity within the Erinaceidae family.Our phylogenetic analyses revealed widespread cryptic divers... In Zeng et al.(2024),we employed mitochondrial genome sequencing to investigate the evolutionary history and cryptic diversity within the Erinaceidae family.Our phylogenetic analyses revealed widespread cryptic diversity,particularly within the genus Hylomys of the subfamily Galericinae.This study proposed that several Hylomys subspecies likely merit full species status and identified two potentially unrecognized subspecies:Hylomys suillus ssp.1 and H.suillus ssp.2(Figures 1-3 in Zeng et al.2024). 展开更多
关键词 Hylomys cryptic diversity Erinaceidae erinaceidae familyour phylogenetic analyses genus hylomys mitochondrial genome sequencing
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Transcript diversity in aging: cryptic transcription and splicing 认领 引用
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作者 Brenna S.McCauley Nicholas Nikoloutsos Weiwei Dang 《Medical Review》 2025年第5期400-411,共12页
Increased transcript diversity,which is caused in part by alternative splicing and cryptic transcription,is an underappreciated aspect of age-associated transcriptome remodeling.Recent work has revealed that structura... Increased transcript diversity,which is caused in part by alternative splicing and cryptic transcription,is an underappreciated aspect of age-associated transcriptome remodeling.Recent work has revealed that structurally novel transcripts increase during aging in many tissues.Genes with cryptic and alternatively spliced transcripts with age are enriched for functional categories relevant to tissue function and aging,and have been implicated in cognitive decline,decreased muscle strength,reduced oocyte quality,immune aging,altered stem cell properties,and senescence.Indeed,there is emerging evidence that alternatively spliced transcripts and elevated cryptic transcription directly contribute to aging phenotypes in multiple tissues.The full impact of the increased transcript diversity on the aging process has yet to be explored.The increased transcript diversity engendered by alternative splicing and cryptic transcription is emerging as a potent driver of aging and aging phenotypes,adding another layer to our understanding of the transcriptional regulation of aging. 展开更多
关键词 aging alternative splicing cryptic transcription epigenetics
Integrative phylogenetic and morphological approach for species delimitation of Heliopora corals,with the description of H.chinensis sp.nov.(Octocorallia:Helioporidae) 认领 引用
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作者 Jingjing Zhang Yisi Hu +6 位作者 Lin Yang Zhiwei Zhang Shichao Wei Wen Yu Hao Luo Fuwen Wei Wenliang Zhou 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第4期601-611,共11页
Heliopora(subclass Octocorallia,order Scleralcyonacea,family Helioporidae),commonly known as the“blue coral,”represents the only reef-building lineage within Octocorallia.The genus shows diverse growth forms of bran... Heliopora(subclass Octocorallia,order Scleralcyonacea,family Helioporidae),commonly known as the“blue coral,”represents the only reef-building lineage within Octocorallia.The genus shows diverse growth forms of branching,encrusting,and laminar types,which leads to ambiguities in traditional morphology-based taxonomy.Here,we investigated the diversity of Heliopora species in the South China Sea(SCS)and their phylogenetic relationships across the Indo-Pacific using integrated morphological and phylogenomic approaches.Whole-genome resequencing of 52 colonies from the SCS islands,combined with published data from 244 samples worldwide,revealed three distinct clades:H.coerulea,H.hiberniana,and a previously undescribed lineage.Morphological analyses characterized the new lineage with a blue skeleton,a short columnar to encrusting growth form,large autopores with 12-15 pseudosepta,absence of worm tubes,and elaborated coenchymal echinulations.These features contrast with the long-branching to lobate H.coerulea and the white-skeletoned H.hiberniana.Based on its unique morphology and distinct phylogenetic position,we describe this lineage as a new species:Heliopora chinensis sp.nov.It is distributed mainly in the SCS islands,Taiwan of China,and the Ryukyu Islands.Meanwhile,global research and citizen science records suggest that H.hiberniana is restricted to the lower latitudes of Indo-Pacific Ocean,whereas H.coerulea occurs broadly across the Indo-Pacific.Our findings highlight the effectiveness of integrating phylogenomics and morphology to resolve coral systematics,uncover cryptic species diversity,and provide new insights into speciation,diversification,and conservation of corals,thus providing a critical taxonomic basis for informing future conservation strategies for coral reef ecosystems. 展开更多
关键词 blue coral cryptic diversity Heliopora phylogenomics species delimitation
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