U.Taxonstand:An R package for standardizing scientific names of plants and animals

The scientific names of organisms are key identifiers of plants and animals.Correctly treating scientific names is a prerequisite for biodiversity research and documentation.Here,we present an R package,’U.Taxonstand’,which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success.Unlike most of other similar R packages each of which works with only one taxonomic database,U.Taxonstand can work with all taxonomic databases,as long as they are properly formatted.Multiple databases for plants and animals that can be directly used by U.Taxonstand,which include bryophytes,vascular plants,amphibians,birds,fishes,mammals,and reptiles,are available online.U.Taxonstand can be a very useful tool for botanists,zoologists,ecologists and biogeographers to standardize and harmonize scientific names of organisms.

Are the altitudinal patterns of plant diversity derived from field surveys consistent with those from empirical integrated methods?

Field surveys and empirical integrated methods are commonly used in the ecological research to understand the altitudinal pattern of plant diversity of mountains.However,few studies have compared the differences between the two methods on the same scale.Here,we addressed and compared the altitudinal patterns of species richness(SR),phylogenetic diversity(PD),the standardized effect size of phylogenetic diversity(PDses)and mean phylogenetic distance(MPDses)of about 580 angiosperms growing on Mount Kenya from two independent datasets:one is based on our several times field surveys in this mountain and another one is based on empirical data integrated from literatures.We found that the altitudinal diversity patterns of field surveys dataset were consistent with the empirical integrated dataset.Both SR and PD showed hump-shaped patterns along the altitude,and both PDses and MPDses showed monotonically decreasing patterns along the altitude.The ratio of diversity between field surveys dataset and empirical integrated dataset were gradually increase along the altitude.Our research provides new insight for understanding the altitudinal diversity patterns of plants of a tropical mountain.

Seasonal implications for taxonomic sufficiency to simplify M-AMBI methodology in the coastal area adjacent to a eutrophic estuary

Taxonomic sufficiency(TS)refers to identifying taxa to a taxonomic level sufficient to detect community changes in stressed environments and may provide a cost-effective approach in routine monitoring programs.However,there is still limited information regarding the seasonal impact of applying TS and its implications for the ecological quality evaluation in the estuarine ecosystem.This study investigated the relationship between the multivariate-AZTI’s Marine Biotic Index(M-AMBI)and environmental variables in three seasons(i.e.,spring,summer,and autumn)in the Liaohe River Estuary.We tested the reliability of TS for simplifying the M-AMBI methodology.The results showed that family and genus level data could reproduce the spatial-temporal patterns of community structure at the species level.The M-AMBI values showed a consistent spatial distribution pattern in all sampling seasons,with a decreasing trend with the increasing distance from the estuary mouth.Both genus and family level data performed nearly as well as species level in detecting the seasonal variations of pollutants(i.e.,nutrients and total organic content).The family level M-AMBI was feasible to discern stress in the Liaohe River Estuary because of the high aggregation ratios at different taxonomic levels in all sampling seasons.These findings suggest that applying taxonomic sufficiency based on the M-AMBI provides an efficient approach for evaluating ecological quality in the Liaohe River Estuary.

Taxonomic revision of genus Rohanixalus(Anura:Rhacophoridae)in China with description of one new species

DEAR EDITOR,Based upon morphological and molecular evidence,the authors revised the genus Rohanixalus Biju,Garg,Gokulakrishnan,Chandrakasan,Thammachoti,Ren,Gopika,Bisht,Hamidy and Shouche,2020(Anura:Rhacophoridae)in China through describing one new species,adding one species to the fauna(R.shyamrupus)and supplementing data on one species(Rohanixalus hansenae;Supplementary Materials).

Redefinition of the Odorrana versabilis Group,with a New Species from China(Anura,Ranidae,Odorrana)

Taxonomic studies of the Odorrana versabilis group have been consistently disorganized,and they have often been incorrectly associated with an abandoned subgenus or genus Bamburana in existing literature.In this study,we conducted an integrative taxonomic analysis using molecular phylogenetic analysis of two mitochondrial gene fragments(16S rRNA and CO1)and morphological examination of 41 specimens collected during herpetological surveys in southern China.Our results confirmed the monophyly of O.versabilis group which exhibited distinct morphological traits.We also identified a cryptic lineage sister with O.exiliversabilis.Additionally,our study revealed that O.trankieni was nested within O.nasuta.Consequently,we redefined the morphological characteristics of the O.versabilis group,described a new species in this group,O.confusa sp.nov.,and proposed that O.trankieni be considered a junior synonym of O.nasuta.One of the most significant findings of this study was the observation of distinct morphological changes in adult males across all species within the O.versabilis group between the non-breeding and breeding seasons.This study contributes to research on various aspects of Asian amphibian fauna,including taxonomy,ecology,evolution,and physiology.

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.

New Advances in Plant Biology Research on Reevesia Lindley

Reevesia spp.are rare and precious trees full of characteristics.China is the geographical distribution center of Reevesia Lindley in the world,but all the plants of Reevesia Lindley are wild with very small number,which is worth developing and utilizing.This study reviews the recent advances in the study of Reevesia Lindley,including morphological characteristics and taxonomic status,plant species and geographical distribution,biology and humanistic sociological values,as well as population ecology and reproductive biology.

Description of Four New Species for the Genus Damasippus Stål, 1875 (Phasmida: Prisopodidae)

During the review and identification of specimens of the genus Damasippus Stål, 1875 deposited in the National Museum of Costa Rica, some specimens were found that corresponded to four non-described species: D. sepia n.sp., D. viridicorpus n.sp, D. duoviridis n.sp and D. viridilabrum n. sp. Due to the above, a review of the literature describing the species of this group was carried out, with which an illustrated dichotomous key was developed to identify the 16 species, in addition to a partial phylogenetic analysis to corroborate that they do not correspond to the species D. fuscipes, due to its morphological similarity.

从Fuzzy Taxonomic数值型数据库中挖掘一般化关联规则

挖掘关联规则是数据挖掘研究的一个重要方面 基于属性内通常还存在更高层次的抽象 ,即呈现出Taxonomic结构这一事实 ,Srikant和Agrawal等人提出了在确定的Taxonomic结构下挖掘泛化布尔型关联规则的挖掘算法 但在实际应用中 ,往往这种Taxonomic结构还呈现出模糊性 ;着重研究了在这种模糊Taxonomic结构下如何从数值型数据库中挖掘一般化关联规则的问题 ,提出了一种新的FuzzyTaxonomic数值型数据库模型 ,并提出了相应的规则发现方法 。

Secondary Metabolites of the Genus Trichilia:Contribution to the Chemistry of Meliaceae Family

According to the literature data on the chemical composition of the Trichilia genus performed in this work, it can be concluded that 334 different compounds were isolated and identified, distributed in monoterpenes, sesquiterpenes, diterpenes, triterpenes, steroids, limonoids, coumarins, flavonoids, lignans, phenolic acids, amino acids and lactones. Together with the structures of this compound, data from botanical classification and pharmaco-logical results from extracts and pure compounds on the Trichilia genus were also described. The compounds derived from terpenes pathway were more significant, corresponding to about 87.7% of isolated and identified compounds from various Trichilia species. Among the different terpenoid skeletons of this kind, limonoids were meanly reported, appearing a total of 33.9% of compounds isolated from several Trichilia species.

Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence

At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed accord- ing to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as out- groups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present （YBP）, and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.

Genetic Relation Analysis on Ramie[Boehmeria nivea(L.)Gaud.]Inbred Lines by SRAP Markers

The objective of this article is to reveal the variations of ramie inbred lines in DNA level and discuss their molecular background to provide a theoretical basis for ramie cross breeding. In the present study, the genetic relationships among 33 inbred line accessions and two wild types that originated from China and Brazil were estimated using sequence-related amplified polymorphism （SRAP） markers. The results showed that 33 out of 81 primer combinations turned out to be polymorphic and 332 polymorphism bands were obtained. On the basis of the appearance of the markers, the genetic relationships were analyzed using unweighted pair-group method of arithmetic average cluster analysis （UPGMA）, and the genetic Jaccard similarity coefficients were calculated. The inbred-lines originating from China and Brazil formed a cluster suggesting a possibility that the Brazilian cultivars could have developed from cultivars introduced from China. Within ramie inbred-lines, the groupings also indicated that the greatest genetic relationship among cultivars was correlated to the region of origin of cultivars. The results provided the evidence that SRAP was an efficient approach, suitable for taxonomic analysis of ramie inbred lines, To the authors＇ knowledge, this is the first application of SRAP marker on the systematics of ramie inbred lines.

Resurrection of the Genus Leptomantis, with Description of a New Genus to the Family Rhacophoridae(Amphibia:Anura)

Genus Rhacophorus Kuhl and Van Hasselt, 1 822 is one of the most diverse genera of the family Rhacophoridae, and its taxonomy of genus Rhacophorus faces major challenges because of rapidly described new species and complex interspecies relations. In this study, we investigate the generic taxonomy within the genus Rhacophorus based on 1 972 bp of mitochondrial genes(12S rRNA, tRNA-val and 16S rRNA), containing 102 sequences from 58 species. The results reveal three well-supported and highly diverged matrilines that correspond with morphological characteristics and geographic distribution. Accordingly, we consider these three lineages as distinct genera: Rhacophorus sensu stricto, resurrected genus Leptomantis Peters, 1867, and the genus Zhangixalus gen. nov.

Biogenic VOCs emission inventory development of temperate grassland vegetation in Xilin River Basin, Inner Mongolia, China

Given the key role of biogenic volatile organic compounds(VOCs) to tropospheric chemistry and regional air quality, it is important to generate accurate VOCs emission inventories. However, only a less fraction of plant species, in temperate grassland of Inner Mongolia, has been characterized by quantitative measurements. A taxonomic methodology, which assigns VOCs measurements to unmeasured species, is an applicable and inexpensive alternation for extensive VOCs emission survey, although data are needed for additional plant families and genera to further validate the taxonomic approach in grassland vegetation. In this experiment, VOCs emission rates of 178 plant species were measured with a portable photoionization detector(PID). The results showed the most of genera and some families have consistent feature of their VOCs emission, especially for isoprene, and provide the basic premise of taxonomic methodology to develop VOCs emission inventories for temperate grassland. Then, the taxonomic methodology was introduced into assigning emission rate to other 96 species, which no measured emission rates available here. A systematical emission inventory of temperate grassland vegetation in Inner Mongolia was provided and further evidence that taxonomy relationship can serve as a useful guide for generalizing the emissions behavior of many, but not all, plant families and genera to grassland vegetation.

Freeliving marine nematodes as a pollution indicator of the Bohai Sea

A hierarchical diversity index—taxonomic distinctness index Δ +, which was first defined by Warwick and Clark in 1998, was employed to evaluate the pollution status of the Bohai Sea with freeliving marine nematodes. The result showed that the Bohai Bay and other coastal sampling sites might be affected by oil and gas production and other anthropogenic influences. In other words,anthropogenic disturbance was affecting this component of the benthos in these locations. And most offshore sampling sites in the middle of the Bohai Sea were clear and unpolluted.

Diversity and conservation of Chinese wild begonias

Begonia, one of the most diverse plant taxa and the fifth or sixth largest angiosperm genus, consists of over1800 accepted species. The number of species recognized within this genus has greatly increased over the past 20 years, rising from 80 to 200 species in China alone. Based on recent field surveys, the number of begonia species in China is predicted to be between 250 and 300. Given the large number of begonia species that still remain to be described, further taxonomical work is urgently required. This is especially true for Chinese Begonia, in which there is a huge diversity of habitat, habit, plant size, leaf type, flower and fruit morphology, and most species are narrowly distributed in isolated habitats that are subject to negative disturbances from climate change, as well as agricultural and industrial activities. Although the conservation status for the majority of species has been evaluated using the standards of the International Union for Conservation of Nature, the results don't represent the truth in many species, and also about11.5% of which are data-absent. In addition, illegal collection and over-harvesting of wild begonias for ornamental or medicinal use has increased due to the rapid development of internet commerce. Far more often than predicted, these species should be categorized as rare and endangered and require immediate protection. Ex situ conservation of Chinese begonias started in 1995 and over 60% of the total species have been so far introduced into cultivation by several major botanical gardens in China. However, only few research institutions, limited funds and human resources have been involved in Begonia conservation;moreover, no project has conducted reintroduction. Therefore, more conservation-based work remains to be done. Improved conservation of Chinese begonias in the future depends on further field survey, an improved understanding of population diversity, and integrative approaches, including in situ and ex situ conservation, seed banking, and plant reintroduction. Species-targeted conservation zones should be established for endangered species excluded from the existing nature reserves. Additionally, laws pertaining to plant protection should be extended to prevent the illegal collection and transaction of wild plants, particularly for those species with unique habitats and small populations.

On the Generic Taxonomy of Opisthotropis balteata(Cope, 1895)(Squamata: Colubridae: Natricinae): Taxonomic Revision of Two Natricine Genera

The single prefrontal configuration has historically been used as an important diagnostic character for many natricine taxa. For example, the genus Trimerodytes Cope, 1895 was long been regarded as a junior synonym of Opisthotropis Günther, 1872 for their similar prefrontal configurations and the type species, T. balteatus Cope, 1895, has been assigned to the genus Opisthotropis. However, as the number and arrangement of prefrontal vary frequently both at species and generic level, it is questionable whether the synonymization of Trimerodytes reflects their evolutionary relationships. On the basis of recently collected specimens of O. balteata, the generic status of the species was assessed using both molecular and morphological data. Opisthotropis was recovered as polyphyletic with reference to O. balteata, because O. balteata is nested within the genus Sinonatrix Rossman and Eberle, 1977 and is the sister species of the type species of Sinonatrix. Consequently, we herein resurrect the long-overlooked synonym Trimerodytes from Opisthotropis and synonymize the junior generic nomen Sinonatrix with Trimerodytes. In addition, based on morphological similarities between the monotypic genus Paratapinophis Angel, 1929 and Trimerodytes, we doubt about the validity of Paratapinophis. Following taxonomic changes in this work, the taxonomic account of the genus Trimerodytes, updated descriptions of its type species, and diagnostic key to Trimerodytes species are provided.

Synopsis of Leymus Hochst.(Triticeae:Poaceae)

Leymus is a genus in the Triticeae tribe, Poaceae. The taxa of this genus are allopolyploid species which possess the Ns and Xm genomes. According to cytological, cytogenetic and molecular genetic analyses, some species of Hystrix and Elymus ought to be transferred to this genus. A world revision of the genus Leymus is needed. In this paper we summarize experimental results, provide a key to sections, species and varieties, and list all the taxa we recognize in Leymus with their synonyms. This synopsis is a new taxonomic system to be used for the revision of Leymus.

Adansonia digitata L.(baobab):a review of traditional information and taxonomic description

Adansonia digitata L.(Malvaceae) is commonly known as baobab tree native to Africa.Baobab is a multi-purpose tree which offers protection and provides food,clothing and medicine as well as raw material for many useful items.The fruit pulp,seeds,leaves,flowers.roots,and bark of baobab are edible and they have been studied by scientists for their useful properties.The fruit pulp have very high vitamin C.calcium,phosphorus,carbohydrates,fibers,potassium,proteins and lipids content,which can be used in seasoning as an appetizer and also make juices.Seeds contain appreciable quantities of phosphorus,magnesium,zinc,sodium,iron,manganese,whereas they have high levels of lysine,thiamine,calcium and iron.Baobab has numerous biological properties including antimicrobial,anti-malarial,diarrhoea,anaemia,asthma,antiviral,anti-oxidant and anti-inflammatory activities amongst others.Phytochemical investigation revealed the presence of flavonoids.phytosterols.amino acids,fatty acids,vitamins and minerals.The review summarizes the information on various aspects of traditional information,taxonomic description,medicinal properties and importantly nutritional value.

Taxonomic diversity of fish assemblages in the Changjiang Estuary and its adjacent waters

Taxonomic diversity of fish assemblages in the Changjiang Estuary （Yangtze River Estuary） and its adjacent waters was analyzed based on bottom trawl surveys carried out by R/V Beidou in June, August and October 2006. Four groups of fishes were identified for each survey by the twoway indicator species analysis （TWIA）. Taxonomic distinctness, species richness and phylogenetic diversity were used to detect changes in taxonomic structure of fish assemblages. Most dominant fish species mainly belonged to Perciformes, Pleuronectiformes, Clupeiformes, Scorpaeniformes and Tetraodontiformes. Species richness in offshore waters of the survey area was higher than that in the other area. The average taxonomic distinctness value （AvTD,△^＋） of each fish assemblage was close to the average taxonomic distinctness of master list in the Changjiang Estuary （79.9）, and had a positive correlation with species richness and Shannon diversity index （H′）. A negative correlation was found between variations in taxonomic distinctness （VarTD, A^＋） and traditional diversity indices, which were caused by fish species component that led to longer average path lengths among species. Taxonomic diversity index （△） had the similar results with species richness, Ht, Simpson diversity index （D） and Pielou＇s evenness index （J′）. VarTD also kept stable, which further certificated that fish assemblages and ecological environment were in equilibrium. Taxonomic distinctness index （△^＋） was relatively stable in most of fish assemblages, and had higher values in some fish assemblages for a few absolutely dominant species. The present study showed that fish community formed new equilibrium stability in 2006 in the Changjiang Estuary when compared with those in the corresponding months of annual survey from 1985 to 1986. And AvTD in each sampling station was lower than AvTD of master list in the Changjiang Estuary, so some ecological niches were absent in each sampling stations from taxonomic or phylogenetic relationships, these would be helpful to stock natural resource and maintain ecological equilibruim of fish assemblages.