Levels Of Taxonomic Hierarchy Research Articles

Missing microbial eukaryotes and misleading meta-omic conclusions.

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

Virxicon: a lexicon of viral sequences.

MotivationViruses are the most abundant biological entities and constitute a large reservoir of genetic diversity. In recent years, knowledge about them has increased significantly as a result of dynamic development in life sciences and rapid technological progress. This knowledge is scattered across various data repositories, making a comprehensive analysis of viral data difficult.ResultsIn response to the need for gathering a comprehensive knowledge of viruses and viral sequences, we developed Virxicon, a lexicon of all experimentally acquired sequences for RNA and DNA viruses. The ability to quickly obtain data for entire viral groups, searching sequences by levels of taxonomic hierarchy—according to the Baltimore classification and ICTV taxonomy—and tracking the distribution of viral data and its growth over time are unique features of our database compared to the other tools.Availabilityand implementationVirxicon is a publicly available resource, updated weekly. It has an intuitive web interface and can be freely accessed at http://virxicon.cs.put.poznan.pl/.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels.

A Computational Approach towards Visual Object Recognition at Taxonomic Levels of Concepts.

It has been argued that concepts can be perceived at three main levels of abstraction. Generally, in a recognition system, object categories can be viewed at three levels of taxonomic hierarchy which are known as superordinate, basic, and subordinate levels. For instance, “horse” is a member of subordinate level which belongs to basic level of “animal” and superordinate level of “natural objects.” Our purpose in this study is to take an investigation into visual features at each taxonomic level. We first present a recognition tree which is more general in terms of inclusiveness with respect to visual representation of objects. Then we focus on visual feature definition, that is, how objects from the same conceptual category can be visually represented at each taxonomic level. For the first level we define global features based on frequency patterns to illustrate visual distinctions among artificial and natural. In contrast, our approach for the second level is based on shape descriptors which are defined by recruiting moment based representation. Finally, we show how conceptual knowledge can be utilized for visual feature definition in order to enhance recognition of subordinate categories.

Phytoliths as Emerging Taxonomic Tools for Identification of Plants: An Overview

In the recent advancements in identification of plant species, phytoliths have found an immense role in the identification of plants at different levels of taxonomic hierarchy. Many plant groups are known to accumulate silica in solid form in and between the cells and tissues and hence create the structures commonly known as phytoliths. These phytoliths create replicas of the structures where they are deposited. The shapes of phytolith replicas, their size dimensions (morphometric parameters), surface features (ornamentation), distribution, and orientation pattern in epidermal layers of vegetative and reproductive structures as well as their frequency are highly important for characterization of species. Monocotyledonous families particularly the family Poaceae (Gramineae) are known to produce diverse phytolith types that can serve as diagnostic markers for characterization of different taxa at different levels of taxonomic hierarchy. The present paper highlights the importance of phytoliths in taxonomic analysis of plants particularly in the family Poaceae.

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

BackgroundDeep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group.ResultsCiliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins.ConclusionsOur data indicate a frequent genetic exchange in the deep-sea water above the brines. The “isolated island character” of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).

Does the clash between instinct and science exist in naming nature?

Does the clash between instinct and science exist in naming nature?

Coordinating the traditional and modern approaches in the systematics of insects

The problem of coordinating the traditional and modern approaches to systematics is ever-lasting due to the continuous development and enrichment of our knowledge of biodiversity, means of analysis, and concepts. Comparative morphology was and still is the cornerstone of studies of insect taxonomy. It gives the most extensive and diverse information on the organisms studied, particularly when it is supported by the data on embryology and functional morphology as well as by analysis of adaptive significance of morphological characters. The limitations of this approach are often related to the presence of homoplasies, reversions, etc. Comparative paleontology is the only approach providing direct evidence of the historical succession of taxa and their characters. However, this approach is fully applicable only to some groups due to the specific features of their morphology and taphonomy. All the modern approaches (molecular, cytogenetic, etc.) are very informative but also have their own limitations; they should not be contrasted with the traditional approaches and certainly should not replace them. The traditional approaches do not become obsolete; it is only their comparative importance in the set of taxonomic tools that may be reevaluated. No single approach can be considered universal for an unambiguous reconstruction of phylogeny and substantiation of the natural system of taxa. Each approach has its own advantages and limitations, and only combined use of different approaches allows a broader range of the problems to be solved. Different approaches may prevail in the studies of different groups of insects and at different levels of taxonomic hierarchy. The intuition of the taxonomist, which is so often criticized by the followers of “objective” systematics, is based on taxonomic experience and scope of knowledge of a particular taxon. It does not imply a subjective bias, but allows the taxonomist to choose the instruments adequate to a particular case.

Environmental rRNA inventories miss over half of protistan diversity

BackgroundThe main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers.ResultsWe show that each PCR primer set-specific clone library is not a sample from the community diversity but rather from a fraction of this diversity. Therefore, even sequencing such clone libraries to saturation would only recover that fraction, which, according to the parametric models, varies between 17 ± 4% to 49 ± 10%, depending on the set of primers. The pooled data is thus qualitatively richer than individual libraries, even if normalized to the same sequencing effort.ConclusionThe use of a single pair of primers leads to significant underestimation of the true community richness at all levels of taxonomic hierarchy. The majority of available protistan rRNA gene surveys likely sampled less than half of the target diversity, and might have completely missed the rest. The use of multiple PCR primers reduces this bias but does not necessarily eliminate it.

Predicting microbial species richness

Microorganisms are spectacularly diverse phylogenetically, but available estimates of their species richness are vague and problematic. For example, for comparable environments, the estimated numbers of species range from a few dozen or hundreds to tens of thousands and even half a million. Such estimates provide no baseline information on either local or global microbial species richness. We argue that this uncertainty is due in large part to the way statistical tools are used, if not indeed misused, in biodiversity research. Here we develop a powerful synthetic statistical approach to quantify biodiversity. It provides statistically sound estimates of microbial richness at any level of taxonomic hierarchy. We apply this approach to a large original 16S rRNA dataset on marine bacterial diversity and show that the number of bacterial species in a sample from marine sediments is (2.4 +/- 0.5 SE) x 10(3). We argue that our methodology provides estimates of microbial richness that are reliable and general, have biologically meaningful SEs, and meet other fundamental statistical standards. This approach can be an essential tool in biodiversity research, and the estimates of microbial richness presented here can serve as a baseline in microbial diversity studies.