Comparison of numerical taxonomic methods used to estimate flavonoid similarities in the Limnanthaceae

The Limnanthaceae is a small family of North American herbs with uncertain internal relationships. Taxa of the family were compared on the basis of 46 flavonol glycosides occurring in all plant tissues or in petals only. The flavonoid data were analyzed by 3 numerical taxonomic techniques: 1) clustering by the Weighted Pair Group method considering positive and negative matches (Using Simple Matching coefficient) ; 2) clustering by the Weighted Pair Group method considering only positive matches (using Jaccard coefficient) ; 3) Varimax Factor Analysis with rotation. No significantly different results were produced by the two clustering methods. Factor analysis provided a clearer indication of relationships among taxa of the Limnanthaceae than did conventional clustering analysis. Apparently, ordination of taxa in three dimensions is necessary to accurately express relationships between divergent evolutionary lines of the family since much of the expressed variation in flavonoids cannot be accounted for by a one-dimensional clustering technique.     

Comparison of different methods for diversity ordering

Abstract. The measurement of diversity, one of the most important concepts in present-day ecology, can be improved by methods of diversity ordering which have recently been developed. This ordering is achieved by a D(α) diversity index family. Indices of this family show varying sensitivities to the rare and abundant species as the scale parameter, α, changes. The aim of this paper is to review and assess 12 methods of diversity ordering and discuss their relationships in detail. Two of the methods are new to the ecological literature. The diversity ordering methods are compared as to their effectiveness in graphically displaying the differences of community structure and demonstrating the (non-)comparability of communities. Small, medium and large data sets were used to evaluate the methods. A small artificial data set (five to seven species) and a large semi-artificial data set (31 — 141 species) are used in this paper. The results suggest that Rényi's diversity index family and Logarithmic dominance ordering are the most useful methods for diversity ordering of communities of all sizes. Right-tailsum diversity ordering performs well for small communities.     

New method to characterize microbial diversity using flow cytometry

The majority of microorganisms have yet to be cultivated and represent a vast uncharacterized and untapped resource. Here, we report the utilization of a combination of flow cytometry, cultivation, and molecular genetics to develop new methodologies to access and characterize biodiversity in microbial samples. We demonstrate that fluorescent dyes and combinations of dyes can selectively stain portions of bacterial populations that can be isolated as sub-populations using fluorescence-activated cell sorting (FACS). Microbial sub-populations obtained by FACS differ substantially from the original microbial population, as demonstrated by denaturing gradient gel electrophoresis and determination of 16S rRNA gene sequences. These sub-populations can subsequently be used to inoculate microbial growth media, allowing the isolation of different microbial species from those that can be readily cultivated from the original sample using the same microbial growth media. When this technique was applied to the analysis of activated-sludge and Yellowstone Lake hydrothermal vent samples, comparative analysis of 16S rDNA sequences revealed that FACS allowed the detection of numerous bacterial species, including previously unknown species, not readily detectable in the original sample due to low relative abundance. This approach may result in a convenient methodology to more thoroughly characterize microbial biodiversity.     

Comparison of phenotypic and genotypic taxonomic methods for the identification of dairy enterococci

The purpose of the study was to assess the phenotypic and genotypic taxonomic congruence in order to allow species allocation of dairy enterococci. A total of 364 enterococci isolated from ewes'milk and cheese from four Portuguese Registered Designation of Origin areas and 25 type and reference strains of Enterococcus spp. were characterized by a polyphasic taxonomical approach involving 40 physiological and biochemical tests, whole-cell protein profiles, amplification of 16S-23S intergenic spacer regions (ITS-PCR) and subsequent restriction analysis (ARDRA). Ribotyping was also performed with reference strains and a subset of 146 isolates. Numerical hierarchic data analysis showed that single-technique identification levels increase from the physiological and biochemical tests to the protein approach, being lower with ITS/ARDRA and ribotyping. Cross-analysis confirmed a higher unmatching level in all pairwise combinations involving physiological and biochemical data. Whole-cell protein profiles followed by ITS/ARDRA identified 89% of the enterococci. Reliable identification of enterococci from milk and cheese could be obtained by analysis of whole-cell protein profiles. ITS-PCR can be used to confirm E. durans and E. faecium and ARDRA further confirms E. faecalis. Results revealed E. faecalis, E. durans, E. hirae and E. faecium as the prevalent species, although species prevalence showed some degree of variation among the areas.     

Adapting molecular-genetic methods for studying the taxonomic diversity of microbial communities associated with macrophytes

The combination of molecular-genetic techniques used in the study is applied to investigate microorganisms associated with macrophytes. The method of enzymatic lysis with phenol-chloroform extraction is optimal for the total bacterial DNA isolation from both periphyton organisms and enriched cultures. Amplifying the total DNA on conservative primers at the two-step PCR regime is recommended. An analysis of the taxonomic diversity of the microbial community from biofilm on the reed grass and in the enriched cultures propagated on various growth media has been carried out. The results have revealed a high diversity of periphyton microorganisms associated with reed grass, including representatives of such phylogenetic lines as proteobacteria (α, β, γ, and δ subgroups), Bacteroidetes/Chlorobi, Chlamydiae/Verrucomicrobia, and cyanobacteria. The low diversity of sequences in enriched cultures is represented by dominating genotypes of Cellvibrio with a high percentage of homology and uncultivated bacilla.     

Links between global taxonomic diversity,ecological diversity and the expansion of vertebrates on land

Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.     

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.     

Composition and diversity of endolichenic microfungal communities from saxicolous lichens at Nahal Boker,the central Negev Desert,Israel

We studied the endolichenic fungal communities from saxicolous lichens occupying the cobbles at Nahal Boker, the central Negev Desert, Israel. Overall, 101 species belonging to 64 genera were isolated from 12 lichen species collected in three seasons from the south-facing slope (SFS) and north-facing slope (NFS) of the wadi. The endolichenic communities possessed a set of traits, which helped them to cope with harsh internal and external conditions. It included a prevalence of melanin-containing fungi with thick-walled and multicellular spores and a comparatively high contribution of thermotolerant species and species with meiospore-producing life cycle stage at the more microclimatically severe SFS. Species richness and isolate density of endolichenic communities was the highest in fruticose lichens with thick and wrinkled thalli, and the lowest in endolithic species possessing thin and smooth thalli. The communities from lichens formed a more diverse group than those from surrounding cobbles probably due to the influence of various species of lichens belonging to different growth forms.     

Influence of wildfire on diversity of culturable soil microfungal communities in the Mount Carmel forest,Israel

The fire-related variations in culturable microfungal communities in the soil of the Mount Carmel forest, Israel, were examined by comparing the communities from burned and adjacent unburned soil plots under pine and oak trees – collected 6, 18, and 26 months after the fire. A total of 82 species representing 44 genera were isolated using the soil dilution plate method. The results showed that the fire had strongly influenced the composition and structure of microfungal communities. The fire remarkably changed physical and chemical properties of the environment, decreasing water holding capacity, organic matter and total nitrogen content in the burned soil. These changes supported abundant development of fast-growing mycoparasitic species (Clonostachys rosea and Trichoderma spp.) and caused significant decrease in species richness. The variations in community composition were much more expressed in the burned soils under oak vegetation as compared with the pine trees. In the oak burned soils, the contribution of the “mesic” component, Penicillium spp., was markedly lower, whereas the contribution of the “xeric”, stress-selected component, melanin-containing species, was higher than in the unburned communities. Such variations can be also considered as a community response to the fire-related decrease in water and nutrient content in the burned soils.     

Comparison of the results of PCR-RFLP and reverse hybridization methods used in molecular diagnosis of FMF

Familial Mediterranean fever (FMF) is characterized by recurrent fever, serositis, and arthritis. Due to the abundance of mutations and clinical heterogeneity of the disease, different screening methods have been developed. In this study, we aimed to compare our findings of mutations determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with reverse hybridization (RH) methods. In 152 of 263 patients (57.79%) different mutations were determined with RH. Allelic frequencies were E148Q 6.84%, M680I(G/C) 3.61%, M694V 20.91%, V726A 7.03%, P369S 1.33%, F479L 0.19%, M680I(G/A) 0.76%, M694I 0.57%, K695R 0.57%, A744S 0.38%, R731H 0.38%, and del1692 0%. Frequent mutations were also confirmed by PCR-RFLP. There were no conflicting results between the two methods. Four of these genotypes were homozygous for a single mutation, 15 were heterozygous for two mutations, 8 were heterozygous for a single mutation, 1 was heterozygous for three mutations, and 1 was homozygous for one mutation and heterozygous for another mutation. It has been reported that analytical sensitivity of RH is 97%. We did not find a discrepancy between the two methods. In 21 patients, we detected additional mutations with RH. This finding was regarded as an advantage of RH, and we concluded that this assay is a useful method for detection of first stage FMF mutation screening.     

A novel multiple-site extension to pairwise partitioned taxonomic beta diversity

Our understanding of the causes of variation in taxonomic composition, or beta diversity, is progressing rapidly, thanks in part to recent methodological advances. For example, methods for partitioning beta diversity into its “replacement” and “richness” components have helped reveal patterns that had been undetected by traditional analyses. These partitioning methods are derived from pairwise dissimilarity measures, and are thus well suited to many conventional beta diversity analyses, including “distance decay” relationships. However, pairwise beta diversity measures have limitations, including their lack of information about taxa that are shared among three or more sites. Recently, a new suite of multiple-site counterparts to the pairwise partitioning measures of beta diversity was proposed, but the pairwise analogs upon which these were based were subsequently criticized, and compelling arguments were presented in favor of other partitioning approaches. Here, we introduce multiple-site partitioning measures that address these shortcomings, and illustrate their desirable properties using numerical simulations. We also provide an empirical example of their utility by analyzing the temporal beta diversity of breeding birds within the conterminous USA. We show that temporal beta diversity is predominantly driven by replacement rather than richness differences, and correspondingly, that correlations between temporal beta diversity and productivity and elevation are driven primarily by the replacement component. Furthermore, in contrast to existing multiple-site measures, we show that richness differences do play an important part in driving overall beta diversity patterns. Our new multiple-site measures therefore complement existing methods for analyzing beta diversity, and are especially suitable when compositional heterogeneity is the response of interest.     

厦门湾大型底栖动物分类学多样性指数及分类充分性

以厦门湾为研究区域,收集2014—2015年大型底栖动物的调查数据,计算了大型底栖动物的分类学多样性指数,分析了分类学多样性指数与传统生物多样性指数的相关性和依从性,并从多个角度探讨大型底栖动物的分类充分性。结果表明,厦门湾大型底栖动物分类多样性指数(Δ)介于6.04—83.71之间,平均值为68.26,站位分布不均匀;分类差异性指数(Δ~*)介于74.27—99.54之间,平均值为84.23;平均分类差异指数(Δ~+)、分类差异变异指数(Λ~+)的理论平均值分别为86.82、345.0,个别站位落在95%置信区间外,表明局部区域环境受到了一定程度扰动。Δ、Δ~*与Margalef指数、Pielou均匀度指数、Shannon-Wiener指数、Simpson指数呈显著相关,而Δ~+、Λ~+与传统多样性指数间无显著相关;分类学多样性指数可作为传统生物多样性指数的补充。种级、属级和科级的同一多样性指数间呈显著线性相关,拟合度较高(多数R2﹥0.9);根据三个分类水平站位的nMDS二维排序图、2-STAGE的相似性和聚类图,种级、属级和科级的群落结构一致性强,属级较种级丢失的信息约8%、科级为20%,因此在条件有限的情况下,大型底栖动物的监测与评价可根据实际的条件和需求适当将生物鉴定放宽至属水平。     

植物雄蕊合生的多样性、适应意义及分类学意义初探

定义并总结了雄蕊合生现象,对雄蕊合生的类型、适应意义、进化及分类学意义进行了初步的讨论和总结.本文定义"雄蕊合生"为,花内雄蕊与雄蕊之间部分或整体的结合生长,既包括愈合与黏合,也包括结合紧密的贴生和靠生.根据雄蕊合生部位的不同,将雄蕊合牛分为"花丝合生"、"花药合生"和"花丝花药均合生"等三大类.每一类中还存在着合生程度不同的子类型.雄蕊合生的结构还可能进一步与柱头或花柱合生在一起,形成"合蕊柱"一类的复杂结构.雄蕊合生在裸子植物较进化的科如百岁兰科和买麻藤科中就出现了,在种子植物中集中分布在近50个科内,且从系统关系来看,雄蕊合生各个类型可能发生过多次进化上的反复.在被子植物中,花丝合生类型更多地与较早进化的类群联系在一起,且多出现在离瓣花中;花药合生及花丝花药均合生则较晚进化,多与有着明显花冠筒的合瓣花伴随出现.这暗示着,雄蕊的合牛结构有可能与花部其他特征一起影响了植物的繁殖过程,具有一定的适应意义.目前,还没有实验研究针对雄蕊合生各个类型开展实验以揭示其发育机制和适应意义.理论上,花丝合乍能增强雄蕊的强度,有时候还形成了围绕子房与花柱的杯状、管状或环状结构,能对子房和花柱有着保护作用且承受传粉者在花内移动的压力:花丝合生还可将雄蕊固定在一个较为稳定的位置,使得花药接触传粉者身体的部位相对固定,减少了花粉浪费.花药合生能将花内花药都集中到同一个位置,花粉接触传粉者身体的同一部位,从而降低花粉损耗和提高异交授粉的准确性.花丝花药均合生可以同时具有以上两种合生方式的适应意义,而且还极大改变了雄蕊的结构与空间位置,改变了花药与柱头之间的空间位置(雌雄异位),对花内自交可能性和雌雄功能干扰有着潜在的影响.雄蕊合生各个类型的适应意义及其对访花者类型与行为和植物繁殖策略的影响,还需要开展实验进行针对性的研究.由于雄蕊形态与结构较为稳定,雄蕊合生的不同方式以及合生程度可以作为科与种的分类参考.     

Patterns of taxonomic diversity among terrestrial isopods

The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics.