The significance of the Northern Andes for lichens

Evaluation of the lichen flora of the Northern Andes must be based on a restricted number of better-known groups, probably less than 25% of the flora. This is because our knowledge of the taxonomy and distribution of lichens in the Tropics is still very incomplete. In the Andes, the groups with foliose and fruticose growth forms are particularly well represented; the crustose group seems less important. This is in contrast with the surrounding lowlands, where crustose is the dominant growth form. At higher taxonomic levels there is a resemblance in taxonomic composition with the cooler zones of the world, which disappears at the generic or sectional levels. A conspicuous morphological feature is the frequency of foliose lichens with linear, rhizinate, or ciliate lobes, probably an adaptation to very humid conditions. More than half of the species have a wide distribution throughout the Tropics or at least in the Neotropics. Among the more restricted taxa is a humid montane element. At the highest elevations a temperate element is apparent, usually with bicentric distribution in both hemispheres. Perhaps 10% of the species are known only from the region; local endemism is probably very scarce. A few taxa appear to be restricted to Ecuador and southern Colombia or Venezuela; so far, only a single species is known with certainty to be restricted to the humid paramos of Colombia. There are distinct affinities with the lichen flora of southeastern Brazil and the Caribbean-Central American area but not with the adjacent Guayana Highland.     

淫羊藿属分类学研究:进展、问题与展望

淫羊藿是我国特有且传统的重要药用植物,逐渐步入大宗品种行列。物种的准确鉴定是药效保障和用药安全的前提,为促进其资源的合理开发和利用,该文对淫羊藿属分类学研究进行系统梳理,并对其中存在的问题及存疑类群进行阐述。淫羊藿属共发表68种,中国58种(85.3%),其中57种为特有分布,具有显著的资源优势。淫羊藿属中国类群的分类学研究较为特殊,共26种集中发表于1990s,共31种(53.4%)为国外研究者命名,且绝大多数依据少量栽培个体命名。由于缺乏广泛的形态调查和性状变异分析,导致大量类群的形态描述不准确或不全面,后续20个类群被归并或降级。依据栽培个体命名的类群是补充描述和分类修订的重点。花色、根茎类型、花茎叶的数量及着生方式等性状在中国类群中存在广泛变异。经分类修订后,该属目前包括46种、1亚种和2变种。淫羊藿属中国组类群仍处于活跃进化中,其形态变异复杂,种间关系无法得到解决,为该属分类的最大挑战。但种质资源的研究和利用需要建立在清晰的分类学基础上。未来研究应基于居群调查,完善各物种的形态描述;在此基础上,整合形态变异特征、地理分布格局和基因序列特征,检测自然种间杂交事件,从而揭示物种的分化和进化历程。     

Integrated taxonomy of the <Emphasis Type="Italic">Asplenium normale</Emphasis> complex (Aspleniaceae) in China and adjacent areas

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.     

DNA barcoding should accompany taxonomy - the case of Cerebratulus spp (Nemertea)

Many issues in DNA barcoding need to be solved before it can reach its goal to become a general database for species identification. While species delimitations are more or less well established in several taxa, there are still many groups where this is not the case. Without the proper taxonomic background/knowledge and corroboration with other kinds of data, the DNA barcoding approach may fail to identify species accurately. The classification and taxonomy of phylum Nemertea (nemerteans, ribbon worms) are traditionally based on morphology, but are not corroborated by an increasing amount of genetic data when it comes to classification either into species or into higher taxa. The taxonomy of the phylum needs to be improved before the full potential of DNA barcoding can be utilized to make sure that valid Linnean names accompany the barcode sequences. We illustrate the problematic situation in the phylum Nemertea by a case study from the genus Cerebratulus.     

The Linnean shortfall in oceanic island biogeography: a case study in the Azores

Aim Speciation processes on islands are still poorly understood. Previous studies based on the analysis of distribution data from checklists found that the flora of the Azores archipelago differs from other island floras in the exceptionally low number of radiations and the low number of single‐island endemics. The general mechanism(s) responsible for these apparently unique patterns remained unclear. One possible explanation for the distinctiveness of the Azorean endemic flora is the lack of a consistent and critical taxonomic framework for the floras of the Atlantic archipelagos. In this study, molecular variation within a range of Azorean endemic plant lineages was analysed to determine whether inadequacies in the current taxonomy of endemics might be an explanation for the unusual diversity patterns observed in the endemic flora of the Azores. Location Azores archipelago. Method Sixty‐nine populations of eight endemic species or subspecies belonging to five genetic lineages were sampled from all Azorean islands but one. Nuclear and plastid DNA regions were sequenced, and relationships among internal transcribed spacer (ITS) region ribotypes established using statistical parsimony. Results Molecular diversity patterns differ from current taxonomic groupings, with all lineages comprising previously overlooked genetic entities. Main conclusions Recognition as distinct taxa of the genetically distinct entities discovered in this study would drastically change the diversity patterns and make them more similar to those of other Atlantic archipelagos. The results serve to highlight that current knowledge of endemic diversity on oceanic islands may be far from complete, even in relatively well‐known groups such as angiosperms. This limitation is rarely considered in macroecological and evolutionary studies that make use of data from taxonomic checklists to draw inferences about oceanic island biogeographic processes.     

Some problems of the study and representation of Siberian flora biodiversity in connection with its conservation

The present knowledge of flora of Siberia is quite insufficient, which is a considerable obstacle to the detection of its biodiversity for conserving the gene pool. Planning conservation measures should be focused not only on species, but also on intraspecific taxa and their phylogenetic uniqueness. In the absence of genetic data, available morphological and geographical methods should be used, so that, when it is impossible to establish the actual origin and relationship of taxa, the existing morphological diverstity is at least represented, as far as it is known to be based on genetic diversity. Phenetic maps can be of much use in the study of intraspecific morphological diversity. The estimation of geographic variability and morphological diversity, as well as the evaluation of territories, can be based on such maps. To represent adequately the biodiversity existing within poorly studied, presumably hybrid plant groups, until actual origin and relationship are known, they should probably be forcedly and provisionally considered as a special type of hybrid complexes, representing the unclear present day taxonomic situation. Such complexes could include populations and individuals with morphological characters of two or more different species, until the systematic position of such populations and individuals is further explored. Until the actual taxonomic status and relationship of the components are established, they could be regarded as subspecies permitted by the Code, or as certain recorded morphological deviations from the type, without assigning any taxonomic status to them--depending on the available data on variability and distribution. In the future, the resulting provisional information on morphological diversity would help to concentrate the efforts of biologists, in possession of the newest methods, on the most important objects, and serve as the scientific base for effective measures aimed at the conservation and management of the vast gene pool of the Siberian flora.     

When taxonomy meets genomics: lessons from a common songbird

Taxonomy is being increasingly informed by genomics. Traditionally, taxonomy has relied extensively on phenotypic traits for the identification and delimitation of species, though with a growing influence from molecular phylogenetics in recent decades. Now, genomics opens up new and more powerful tools for analysing the evolutionary history and relatedness among species, as well as understanding the genetic basis for phenotypic traits and their role in reproductive isolation. New insights gained from genomics will therefore have major effects on taxonomic classifications and species delimitation. How a genomics approach can inform a flawed taxonomy is nicely exemplified by Mason & Taylor ( 2015 ) in this issue of Molecular Ecology. They studied redpolls, which comprise a genus (Acanthis) of fringillid finches with a wide distribution in the Holarctic region, and whose species taxonomy has been a matter of much controversy for decades (Fig.  1 ). Current authoritative checklists classify them into one, two or three species, and five or six subspecies, based largely on geographical differences in phenotypic traits. Previous studies, including a recent one of the subspecies on Iceland (Amouret et al. 2015 ), have found no evidence of differentiation between these taxa in conventional molecular markers. The lack of genetic structure has been interpreted as incomplete lineage sorting among rapidly evolving lineages. Now Mason & Taylor ( 2015 ), using a large data set of genomewide SNPs, verify that they all belong to a single gene pool with a common evolutionary history, and with little or no geographical structuring. They also show that phenotypic traits used in taxonomic classifications (plumage and bill morphology) are closely associated with polygenic patterns of gene expression, presumably driven by ecological selection on a few regulatory genes. Several lessons can be learned from this study. Perhaps the most important one for taxonomy is the risk of taxonomic inflation resulting from overemphasizing phenotypic traits under local adaptation and ignoring a lack of phylogenetic signal in molecular markers.     

The current systematics and taxonomy of the powdery mildews (Erysiphales): an overview

A brief survey of the current systematics and taxonomy of powdery mildews (Erysiphales) is given with special focus on new characters used for taxonomic purposes as well as new approaches, methods and techniques. The structure of the family Erysiphaceae based on phylogenetic results is summarized, and the current, strongly increased number of powdery mildew taxa in a planned new monographic treatment of this fungal group is given and compared with the old monograph from 1987.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

The round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species.     

A botanical critique of cladism

Clade versus grade is an old question in taxonomy, going back as far as Darwin himself. Taxonomists have long believed that both must be taken into account in the formation of a general-purpose system. Recently clade has been elevated to a position of total dominance by a group of taxonomists who take their inspiration from Willi Hennig. Mayr has dubbed this approach cladism, and its exponents cladists. Cladistic theory is being vigorously developed and propounded by Hennig’s disputatious disciples, and much of the present-day theory would scarcely be recognized by the founder. I here address myself to what I consider the core features of present-day cladism. The essential distinctive feature of cladism, and its fatal flaw, is that a group is considered to be monophyletic, and thus taxonomically acceptable, only if it includesall the descendants from the most recent common ancestor. The traditional taxonomic view has been that a group can still be considered monophyletic (and thus taxonomically acceptable) after some of its more divergent branches have been trimmed off. This simple and seemingly innocuous difference has profound consequences to the taxonomic system. In Hennigian classification, organisms are ranked entirely on the basis of recency of common descent, that is, on the basis of the sequence of dichotomies in the inferred phylogeny. Theamount of divergence scarcely enters into the picture. This procedure represents an effort to capture taxonomy for a narrowly limited special purpose, at the expense of the important and necessary function of providing a general-purpose system that can be used by all who are concerned with similarities and differences among organisms. The first corollary of the Hennigian concept of phylogenetic taxonomy is that no existing taxon can be ancestral to any other existing taxon. The descendant must be included in the same taxon as its ancestor. At the level of species this is palpably false. The ancestral species often continues to exist for an indefinite time after giving rise to one or more descendants. At the higher taxonomic levels adherence to the principle often requires excessive lumping or excessive splitting to avoid paraphyletic groups (i.e., groups that do not include all of their own descendants), and it forbids the taxonomic recognition of many conceptually useful groups. Neither the prokaryotes nor the dicotyledons form a cladistically acceptable taxon, since both are paraphyletic. The prokaryotes are putatively ancestral to the eukaryotes, and the dicotyledons are putatively ancestral to the monocotyledons. Many other traditional and readily recognizable taxa would have to be abandoned, without being replaced by conceptually useful groups. Fossils present a special problem, because the whole concept of cladistic classification depends on the absence of taxa at the branch points of the cladogram. Presumably all of these branch points were at some time in the past represented by actual taxa, which under cladistic theory can neither be assigned to one of their descendants nor treated as paraphyletic taxa. The difficulty is mitigated somewhat by the gaps in the known fossil record. Once it is admitted that paraphyletic as well as holophyletic groups are taxonomically acceptable, there is much value in cladistic methodology. Formal outgroup comparison for the establisment of polarity, and the emphasis on synapomorphies in the construction of a cladogram can both be usefully incorporated into taxonomic theory and practice. These require no revolution in taxonomic thought. There are unresolved problems, however, in how to gather and manipulate the data, and how to interpret the cladogram produced by computers. In any complex group, the computer may produce several or many cladograms of equal or nearly equal parsimony. This is particularly true in angiosperms, among which the extensive evolutionary parallelism casts doubt on the importance of parsimony and may lead to the production of hundreds of such cladograms for a single group. Despite the claims of objectivity and repeatability in cladistic taxonomy, the necessity for some subjective decisions remains. The Wagner groundplan-divergence method has most of the advantages of formal cladism without the most important disadvantages. Wagner accepts paraphyletic taxa in principle, and he casts a wider net for data bearing on the polarity of characters. In complex groups consisting of many taxa, however, both methods retain a strong subjective component in the computer manipulation and in the degree of reliance on absolute parsimony.     

Phenetic and phylogenetic studies based on measurements of Plantago ser. Brasilienses

Numerical taxonomic methods for a programmable pocket calculator are proposed. Operational taxonomic units (OTU's) may be either accepted taxa or single specimens, or a mixture of both. All types of characters are employable. A calculated or estimated common standard deviation and the mean (or reading) define the normal distribution curve for each measurement variable. Similarity between two OTU's is calculated as the overlapping area below their distribution curves. Ninety specimens of Plantago ser. Brasilienses are used as examples. The clusters are finally grouped using both phenetic and several cladistic methods. Results from phylogenetic sys–tematics cannot be used directly in taxonomy because the basic principles are discordant with those in the botanical code.     

Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited

The ultimate goal of taxonomy is to establish a system that mirrors the 'order in nature'. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as 'backbone of prokaryote taxonomy' at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that 'drive' evolution in a given environment. In this context, the 'polyphasic taxonomic approach' should be revisited again, taking into account the novel insights into genomes and other 'omic' sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in-depth taxonomy of the prokaryotes.     

Diversity, biogeography, and photosynthetic pathways of Argusia and Heliotropium (Boraginaceae) in South-West Asia with an analysis of phytogeographical units

South-West and Central Asia are major centres of diversity in the genus Heliotropium . On the basis of detailed taxonomic studies and information gathered from the literature, a synopsis of 61 known species of Heliotropium and two species of Arguzia in the area is given. Iran, with 32 species and 14 (sub)endemic species, has the highest diversity. The photosynthetic pathways of 42 taxa were determined using the isotope composition method. Except for H. marifolium Retz s.l. and H. rariflorum Stocks, all remaining species analysed showed δ¹³C values characteristic for C₃ photosynthesis. Evidently, by contrast with the families Chenopodiaceae and Polygonaceae, the Irano-Turanian area is not an authochthonous region of developing C₄ species in Heliotropium . The distribution maps of 57 taxa are provided and their biogeographical importance is discussed in order to elucidate the distribution patterns in South-West Asia. In the Irano-Turanian region, the Irano-Anatolian province of Zohary, which extends from central Anatolia to the western Himalaya, is a very large and vaguely defined phytochorion that should be split into smaller units. The consideration of southern Iran and adjacent Pakistan as part of the Sudanian or Saharo-Sindian regions ( sensu either Zohary or Léonard) cannot be accepted, because most endemic species in this area are either typical Irano-Turanian or isolated relicts. Furthermore, it is concluded that the Saharo-Sindian flora is not an autochthonous flora; most species are of transgressive origin from the surrounding phytochoria. Finally, a new species, Heliotropium ziegleri Akhani, is described from Iran.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155 , 401–425.     

Floristic composition and endemism pattern of vascular plants in Ethiopia and Eritrea

Traditional attempts to delineate floristic regions are typically based on the qualitative analysis of species distribution, often ignoring the phylogenetic relationships among their taxa. Ethiopia and Eritrea are in the Horn of Africa, known as one of the world's biodiversity hotspots. We quantitatively classified the flora of Ethiopia and Eritrea into meaningful geographical units by analyzing the taxonomic and phylogenetic β‐diversity at genera, total species, and endemic species levels at a scale of 0.5° × 0.5° grid cells. Hierarchical clustering was used to quantitatively delimitate the flora and analysis of similarities was used to test the significant difference between the derived groups in taxonomic composition and phylogenetic relatedness. In total, two floristic subprovinces, five floristic districts, and 13 floristic subdistricts, as well as three centers of species endemism associated with three floristic subdistricts were identified. Our results also showed that the species diversity, endemism, and turnover of the highlands in Ethiopia and Eritrea were much higher than the lowlands, indicating that the floristic differences are closely related to the topography of the East African Rift. In this study, we provided a scientific framework for the composition and relationships of the floristic units in the Horn of Africa, and similarly provided a scientific basis for better conservation of the diversity in this region.     

THE USE OF PROTEIN-SEROLOGICAL CHARACTERS IN THE SYSTEMATICS OF THE FAMILY OLEACEAE

Serological analyses of soluble seed proteins of 12 representative taxa of the family Oleaceae by the techniques of Ouchterlony, presaturation, and immunoelectrophoresis (IEP) yielded complementary taxonomic information. Ouchterlony reactions differentiated among protein extracts of three species, and the combined serological techniques permitted the detection of protein differences of respective taxa of the two subfamilies Jasminoideae and Oleoideae. IEP enabled the separation of the 12 taxa investigated and the distribution into the two subfamilies, by the differential electrophoretic positions of precipitin arcs, which were consistent with members of each of the two subfamilies. Presaturation data, when analyzed by two cluster analysis computer programs, were taxonomically significant. One program, which calculated amalgamation distances from the presaturation data, clustered the 12 taxa into subgroups which corresponded to tribes, and within two groups, which corresponded to two subfamilies. A monothetic clustering program provided theoretical information on evolution of taxa within the family Oleaceae based on serological correspondences obtained from the presaturation data; the subfamily Jasminoideae was found phylogenetically primitive and the subfamily Oleoideae was advanced. Additionally, IEP data supported those theories suggesting that taxa of the Oleoideae evolved from taxa of the Jasminoideae. The groupings of taxa and different information obtained from the cluster analyses of data and all serological techniques reinforced each other, as well as contemporary taxonomic and phylogenetic treatments of taxa of the family Oleaceae. This research demonstrated the taxonomic value of protein-serological data, particularly as applied to the taxonomy of the Oleaceae.     

Ecological integrity of supraspecific taxa and the arctic biota

Some specific features of the development of concepts about integrity (systemic organization) of supraspecific taxa are considered. Several forms of integrity can be distinguished: taxonomic, or genealogical; evolutionary (considering a taxon as a developing system); ecological, or eco-adaptive (manifestation of the properties of a united system in the course of exploring the various conditions and types of environment by the phyletically specified biota). Taxa of different level “behave” as whole units or blocks, forming structural parts of the cenotic and biotic forms of life. The properties of integrity, systemic organization of supraspecific taxa can be displayed by analysis of changes in the structural parameters of the biota related to latitudinal gradients of climatic factors, in phenomena of individualistic distribution, ecological substitution (vicariance) of taxa, and preservation of their ecological functions (adaptive zone) despite the reduced species diversity. The variants of adaptive exploration of high-latitude landscape-zonal conditions are considered using examples from the Arctic flora and fauna.