西藏地衣物种多样性的海拔梯度分析

根据西藏地衣分类和区系的文献资料,对西藏地衣物种多样性的海拔梯度进行了分析。267个分类群按照生长型或者基物被分为六组。每一组地衣的物种丰度随海拔增加呈现单峰曲线形式的变化。多数组物种丰度的峰值出现在海拔3400~3900m之间,对应于山地寒温带针叶林带的上半部分,比尼泊尔对应类群出现极值的海拔要高。此植物带谱内复杂的生态系统可能是物种多样性高的主要原因。壳状地衣物种丰度的峰值出现在5100~5400m区间则可能是因为该区内高大的树木的消失以及具有充裕的阳光。西藏的地衣物种多样性远低于尼泊尔,两地共有的物种数量很少。对西藏地衣物种多样性的调查不充分应当是其主要原因,因此今后中国地衣学工作者应当加强西藏地衣多样性的研究。     

Niche width impacts vertebrate diversification

Aim The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location Global. Methods We obtained the time‐calibrated phylogenies, IUCN conservation status, species distribution maps and climatic data for 2340 species of amphibians, 4563 species of mammals and 9823 species of birds. We computed the niche width for each species as the mean annual temperature across the species range. We estimated speciation, extinction and transition rates associated with lineages with either narrow (specialist) or wide (generalist) niches using phylogeny‐based birth–death models. We also tested if current conservation status was correlated with the niche width of species. Results We found higher net diversification rates in specialist species than in generalist species. This result was explained by both higher speciation rates (for the three taxonomic groups) and lower extinction rates (for mammals and birds only) in specialist than in generalist species. In contrast, current specialist species tended to be more threatened than generalist species. Main conclusions Our diversification analysis shows that the width of the climatic niche is strongly associated with diversification rates and may thus be a crucial factor for understanding the emergence of diversity patterns in vertebrates. The striking difference between our diversification results and current conservation status suggests that the current extinction process may be different from extinction rates estimated from the whole history of the group.     

西藏地衣物种多样性的海拔梯度分析

根据西藏地衣分类和区系的文献资料,对西藏地衣物种多样性的海拔梯度进行了分析。267个分类群按照生长型或者基物被分为六组。每一组地衣的物种丰度随海拔增加呈现单峰曲线形式的变化。多数组物种丰度的峰值出现在海拔3400~3900m之间,对应于山地寒温带针叶林带的上半部分,比尼泊尔对应类群出现极值的海拔要高。此植物带谱内复杂的生态系统可能是物种多样性高的主要原因。壳状地衣物种丰度的峰值出现在5100~5400m区间则可能是因为该区内高大的树木的消失以及具有充裕的阳光。西藏的地衣物种多样性远低于尼泊尔,两地共有的物种数量很少。对西藏地衣物种多样性的调查不充分应当是其主要原因,因此今后中国地衣学工作者应当加强西藏地衣多样性的研究。     

Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae

Although discordance between taxonomic diversity and morphological disparity is common, little is known about the underlying dynamics that drive this decoupling. Early in the history of the Cambrian trilobite family Pterocephaliidae, there was an increase in taxonomic diversity and morphological diversity. As taxonomic diversity declined in the later history of the clade, range of variation stayed high and disparity continued to increase. However, per‐branch rates of morphological evolution estimated from a recent phylogeny decreased with time. Neither within‐trait nor within‐species variation increased or decreased, suggesting that the declining rates of morphological evolution were more likely related to ecological opportunity or niche partitioning, rather than increasing intrinsic constraints. This is further supported by evidence for increased biofacies associations throughout the time period. Thus, the high disparity seen at low taxonomic diversity late in the history of this clade was due to extinction – either random or targeting mean forms – rather than increased rates of morphological evolution. This pattern also provides a scenario that could account for instances of low taxonomic diversity but high morphological disparity in modern groups.     

Molecular taxonomic tools provide more accurate estimates of species richness at less cost than traditional morphology-based taxonomic practices in a vegetation survey

Vegetation surveys are conducted to obtain a catalogue of the plant species that occupy an area of interest, and are used to inform the decisions of policymakers about conservation, development, and remediation efforts. Currently, vegetation surveys rely on traditional morphology-based taxonomic practices to identify collected specimens. By implementing recent advances in molecular taxonomy, it may be possible to improve upon these methods and reduce the associated costs. In this study, we used both morphological and molecular taxonomic methods to sample 337 forest vegetation plots in northeastern Ontario, Canada. DNA barcoding—a molecular taxonomic tool—was used to identify specimens collected in the molecular taxonomic survey. The molecular taxonomic survey identified a mean of 12.4 species per plot and 202 species in total, whereas the morphological taxonomic survey identified a mean of 9.8 species per plot and 142 species in total; both surveys provided identical estimates of community similarity. The morphological taxonomic survey was 37 % more expensive than molecular taxonomic survey, owing largely to the increased time required in the field to collect specimens that flowered at different times. Our results indicate that molecular taxonomic tools are more cost-effective than traditional morphology-based taxonomic practices for species identification in vegetation surveys. Taxonomy underpins all conservation, and the implementation of molecular taxonomic tools for vegetation surveys has promise to lessen the consequences of the taxonomic impediment and increase the effectiveness of conservation efforts.     

Molecular Phylogeny and Biogeography of Petaurista Inferred from the Cytochrome b Gene,with Implications for the Taxonomic Status of P. caniceps,P. marica and P. sybilla

The polymorphic genus Petaurista includes a group of diverse species and subspecies that are adapted for gliding and arboreal life. This morphological diversity has resulted in taxonomic discrepancies, and molecular phylogenetic studies have been limited by taxon sampling. To clarify this controversial taxonomy, we used the cytochrome b gene to reconstruct the phylogeny to obtain a more accurate picture of the evolutionary relationships, species differentiation and divergence pattern of Petaurista. The results revealed a significant inconsistency between taxonomic designations, phylogeny and genetic distances. When 6 recognized species were included, species delimitation revealed 15 putative species, a finding that warrants a comprehensive morphological diagnosis and a re-assessment of the species status. The validity of P. caniceps and P. marica was discussed. An estimation of the molecular divergence time demonstrated that the diversification and speciation of Petaurista began during the later Miocene and may have been affected by the uplifting of the Qinghai-Tibet plateau and subsequent climate change.     

基于模式产地的分子证据澄清南平鳞毛蕨的分类学地位

地球上有多少物种一直以来都是人们极度关注的问题, 而存疑物种是造成该问题难以解决的重要阻碍之一。目前, 模式标本是存疑物种得以确定的唯一凭证标准, 然而, 因其特殊的分类学地位而难以进行有效的观察和研究。因此, 前往模式产地寻找存疑物种的原始信息成为最有效的替代途径。随着分子生物学, 特别是DNA条形码技术在物种分类与鉴定中的广泛应用, 准确而快速鉴定存疑物种成为可能。以存疑物种——南平鳞毛蕨(Dryopteris yenpingensis)为例, 利用来自模式产地的分子数据进行DNA条形码分析, 并结合形态学特征澄清了南平鳞毛蕨的分类学地位, 确定南平鳞毛蕨与荔波鳞毛蕨(D. liboensis)为同一物种, 同意将荔波鳞毛蕨作为其异名。研究结果和方法可为今后澄清更多存疑物种的分类学地位提供参考。     

An information-theoretical measure of taxonomic diversity

Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs.     

Review: Taxonomy of Nitella (Charales, Charophyceae) based on comparative morphology of oospores and multiple DNA marker phylogeny using cultured material

The genus Nitella is the largest group in the Charales and has the highest diversity of vegetative and oospore morphologies. In his worldwide monograph on the Charales, R. D. Wood characterized the sections and species of Nitella mainly on the basis of vegetative morphology and treated oospore wall morphology as diagnostic at the infraspecific level. Therefore, many species of Nitella exhibiting distinct external morphology of the oospore wall (EMOW) were reduced to infraspecific rank and only 53 of 204 species previously described were recognized within Nitella . However, recent morphological and molecular phylogenetic studies have demonstrated the phylogenetic validity of using EMOW for diagnosing some species of Nitella . More recently, a scanning electron microscopy (SEM) study of internal morphology of the oospore wall (IMOW) and multiple DNA marker analyses using both nuclear and chloroplast gene sequences were conducted to improve our understanding of the taxonomy of Nitella at the species level, on the basis of cultured material of a large number of species. Multiple DNA marker analyses resolved detailed and robust phylogenetic relationships within the genus and demonstrated the taxonomic and phylogenetic significance of IMOW. In addition, they supported the taxonomic decisions based on differences in oospore morphology, suggesting that an integrated approach, involving both SEM studies of the EMOW and IMOW and multiple DNA marker analyses, is appropriate to address problems at lower taxonomic levels within the genus, as well as to construct a natural taxonomic system for the genus. In this paper, recent morphological and molecular phylogenetic studies are reviewed and recent improvements in taxonomy of Nitella are summarized. Moreover, the evolution of morphological features and phylogenetic relationships within Nitella are discussed, focusing especially on oospore morphology.     

Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island,France)

Diatoms are excellent ecological indicators of water quality because they are broadly distributed, they show high species diversity and they respond rapidly to human pressures. In Europe, the Water Framework Directive (WFD) gives the legal basis for the use of this indicator for water quality assessment and its management. Several quality indices, like the Specific Polluosensitivity Index (SPI), were developed to assess the ecological quality status of rivers based on diatom communities. It is based on morphological identifications and count of diatom species present in natural biofilms using a microscope. This methodology requires high taxonomic skills and several hours of analysis per sample as 400 individuals must be identified to species level. Since several years, a molecular approach based on DNA metabarcoding combined to High-Throughput Sequencing (HTS) is developed to characterize species assemblages in environmental samples which is potentially faster and cheaper. The ability of this approach to provide reliable diatom inventories has been demonstrated and its application to water quality assessment is currently being improved. Despite optimization of the DNA metabarcoding process with diatoms, few studies had yet extended it at the scale of a freshwater monitoring network and evaluated the reliability of its quality assessment compared to the classical morphological approach.In the present study we applied DNA metabarcoding to the river monitoring network of the tropical Island Mayotte. This island is a French département since 2011 and the WFD has to be applied. This offered the opportunity to scale up the comparison of molecular and morphological approaches and their ability to produce comparable community inventories and water quality assessments. Benthic diatoms were sampled following WFD standards in 45 river sites in 2014 and 2015 (80 samples). All samples were submitted in parallel to the molecular and the morphological approaches. DNA metabarcoding was carried out using Genelute DNA extraction method, rbcL DNA barcode and PGM sequencing, while microscopic counts were carried out for the classical methodology. Diatom community structures in terms of molecular (OTUs) and of morphological (species) were significantly correlated. However, only 13% of the species was shared by both approaches, with qualitative and quantitative variation due to i) the incompleteness of the reference library (82% of morphological species are not represented in the database), ii) limits in taxonomic knowledge and iii) biases in the estimation of relative abundances linked to diatom cell biovolume. However, ecological quality status assessed with the molecular and morphological SPI values were congruent, and little affected by sequencing depth. DNA metabarcoding of diatom communities allowed a reliable estimation of the quality status for most of the rivers at the scale of the full biomonitoring network of Mayotte Island.     

Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC

Crassulaceae (orpine or stonecrop family) is the most species-rich (ca. 1400 spp) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and large number of species complicates systematics of the family and obscures reconstruction of relationship within it. Phylogenetic analyzes based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies on the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera are discussed. It is shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analyzed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.     

An update to modern taxonomy (2011) of freshwater planktic heterocytous cyanobacteria

It is essential for the modern taxonomic classification of cyanobacteria to be continually updated in accordance with revisions based on molecular sequence comparisons and combined with morphological features, ecophysiological characters and other biochemical and molecular markers (“polyphasic approach”). Several genera, which are characterized by their planktic life form and contain indicator species important for the evaluation of aquatic biocenoses in majority of water bodies are recognized in the monophyletic group of heterocytous cyanobacteria. Current taxonomic revisions (and nomenclatoric consequences) of the specific contents of these heterocytous cyanobacterial generic units are covered by this article. Among these genera, 12 contain only planktic species, three remaining genera contain both planktic and non-planktic species. Comments and suggestions for future research are stressed especially in the ecologically distinct genera, which includes species dominating in the plankton of various reservoir types.     

Levels of diversity in endomycorrhizal fungi (Glomales,Zygomycetes) and their role in defining taxonomic and non-taxonomic groups

Diversity in glomalean fungi is manifested at the molecular, morphological, and ecological levels. Characters at any of these levels can be ordered into hierarchical patterns defining taxonomic groups if they are conserved enough to be heritable through geologic time in all descendants of a common ancestor. At present, only morphological characters associated with mode of spore formation and in subcellular structure of spores are sufficiently stable and diverse to recognize at least 150 species. Ontogenetic comparisons indicate that species integrity, despite asexual reproduction, is the result of rigid internal constraints imposed on variation during the process of spore subcellular differentiation. Epigenetic factors dominate because the differentiation sequence is linear and each new stage is causally linked to preceding stages. Some morphological characters of the fungal mycelium also exist, but they define more inclusive groups at the family level and above. Most diversity in the mycorrhizae consists of life-history traits associated with abundance and architecture of fungal components, their rate of formation and longevity, and their cost in the symbiosis. These characters participate in processes at the molecular and ecological levels, so they are autonomous from morphological determinants. They often are labile or affected by external environmental conditions, so fewer stable taxonomic characters are likely to be discovered. Instead, molecular and ecological diversity has greater potential to define; (a) niche specificity of organisms/populations and (b) causal processes linked to host-fungus compatibility and mycorrhizal efficiency. Any taxonomic characters that relate to mycorrhizal functions will come only from comparative studies involving organisms from shared habitats rather than those having shared spore morphologies.     

Genetic diversity of ectomycorrhizal Basidiomycetes from African and Indian tropical rain forests

Ectomycorrhizal (ECM) fungi have a worldwide distribution. However, the ecology of tropical ECM fungi is poorly documented, limiting our understanding of the symbiotic associations between tropical plants and fungi. ECM Basidiomycete diversity was investigated for the first time in two tropical rain forests in Africa (Western Upper Guinea) and in Asia (Western Ghats, India), using a fragment of the mitochondrial large subunit rRNA gene to type 140 sporocarps and 54 ectomycorrhizas. To evaluate taxonomic diversity, phylogenetic analyses were performed, and 40 sequences included from identified European specimens were used as taxonomic benchmarks. Five clades were recovered corresponding to six taxonomic groups: boletoids, sclerodermatoids, russuloids, thelephoroids, and a clade grouping the Amanitaceae and Tricholomataceae families. Our results revealed that the Russulaceae species display a great diversity with several putative new species, especially in Guinea. Other taxonomic issues at family/section levels are also briefly discussed. This study provides preliminary insights into taxonomic diversity, ECM status, and biogeographic patterns of ECM fungi in tropical two rain forest ecosystems, which appear to be as diverse as in temperate and boreal forests.     

中国拟家鼠分类与分布厘订

拟家鼠(Rattus pyctoris)由Hodgson在1845年命名,其模式产地为尼泊尔。该种的分类地位和是否在中国有分布都存在较大争议。近来有研究认为拟家鼠不分布于我国。2020年,在西藏吉隆县和札达县进行野外调查时采集到7号标本,皮毛、头骨和牙齿的形态特征与尼泊尔的拟家鼠相似,分子系统发育分析支持这些标本为单系(PP=1.0),与模式产地样品C_yt b基因的K2?P遗传距离为0~2.8%,确认这些标本为拟家鼠。这是第一次在我国境内采集到拟家鼠标本,丰富和完善了这个物种的生物地理资料。     

Interspecific plant functional variation prevails over intraspecific variation in driving spider beta diversity

1. Non-trophic interactions between plants and animals can affect community structure and species trait composition. However, it is unclear how changes in intra- and interspecific morphological traits of plant species affect non-trophic interactions at a metacommunity scale. Additionally, whether plant evolutionary history determines taxonomic and functional diversity of plant-dwelling predators is an open question. 2. To address these gaps, this study used a published dataset with spiders dwelling exclusively on bromeliads to investigate if: (i) intra- and interspecific variability in host plant morphological traits affects spider taxonomic and functional diversity; and (ii) bromeliad trait evolution determines present-day patterns of spider trait diversity. 3. Spider and bromeliad traits were measured, and a new statistical framework was used to quantify the response of spider beta diversity to intra- and interspecific variation in bromeliad traits. In addition, bromeliad traits were decomposed across its phylogenetic tree to check whether the current variation in morphological traits of bromeliads is a result of either ancestral or recent diversification. 4. Bromeliad intraspecific variation did not affect spiders, but leaf length variation between bromeliad species had a positive effect on spider functional beta diversity. Interestingly, the most ancestral split between two subfamilies explained most of the variation in bromeliad species, which suggests that spider functional diversity could represent an outcome of bromeliad evolutionary history. 5. Overall, the results of this study suggest that interactions between plants and organisms that do not feed directly on their tissues could be shaped by plant evolutionary history, which in turn suggests that non-trophic interactions can be maintained over time.     

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.     

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

WE CONDUCTED A COMPREHENSIVE MOLECULAR PHYLOGENETIC STUDY FOR A GROUP OF CHAMELEONS FROM MADAGASCAR (CHAMAELEONIDAE: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.     

GEOMETRIC MORPHOMETRICS OF THE SKULL ROOF OF STEREOSPONDYLS (AMPHIBIA: TEMNOSPONDYLI)

Abstract:  Geometric morphometric analysis using relative warps is applied to the skull roof of 62 species of stereospondyls and their closest outgroups (i.e. basal archegosauriforms) from among temnospondyl amphibians. Twenty-one landmarks and five taxonomic groups are used for comparisons. Their skull evolution is quantified in a morphospace defined by two relative warps axes. The majority of groups show poor concordance between morphological and phylogenetic distances. The only exception is represented by Yates and Warren's study of stereospondyl relationships, in which concordance is high. Only basal archegosauriforms and rhinesuchids show significant overlap in morphospace, although this might be due to low sample sizes. Regression of estimated mean disparity against taxon sample size shows that species within both the trematosauroid and the rhytidostean groups are more widely dispersed in morphospace than species belonging to any of the remaining stereospondyl groups. Stereospondyl skull evolution was characterized by divergence between major clades and convergence within those clades. Changes in patterns of morphospace occupation through time agree with the hypothesis of an 'explosive' radiation in the early Early Triassic, after the extinction of basal archegosauriforms at the end of the Permian.