Taxonomic Classification System Research Articles

The amphibians and reptiles of the Northern Selva Lacandona:

Chiapas harbors significant biological and cultural diversity. The region known as Selva Lacandona is an ideal example to study what is called the “biocultural axiom”. This neotropical region is inhabited by multiple indigenous groups, such as the Tsotziles, Tseltales, Tojolabales, Ch’oles, Kanjobales, Chujes, Mames, Lacandones (Hach Winik), and Zoques. The herpetofaunistic diversity of Chiapas is currently represented by 107 species of amphibians and 223 species of reptiles. In the Selva Lacandona region a total of 35 species of amphibians and 90 reptiles has been documented, with some areas still remaining to be formally explored. Traditionally, the use of natural resources by native indigenous communities has been linked to the selective use of those species that have economical, traditional, and/or magical-religious value. Many of these human groups have a deep traditional knowledge about the environment in which they live, as well as the diversity of plant, fungal, and animal species with which they have coexisted over millennia. The Nahá and Metzabok communities are inhabited by the Maya-Lacandón del Norte culture. The objective of this study is to identify the herpetofaunistic species diversity found within the Flora and Fauna Protection Areas (APFF´s) of Nahá andMetzabok. Additionally, we analyzed whether the Lacandones from the north have a herpetofaunistic ethnical taxonomic classification system. A total of 67 species that are recognized by the Lacandones were recorded for both APFFs. The Lacandones del Norte classify the herpetofauna into six groups, i.e., Ak (Turtles), Kan (Snakes), Ayim (Crocodiles), Torok (Lizards), Xut (Frogs), and Be’p (Toads). For Metzabok, the three most frequently mentioned species are Bothrops asper, Boa imperator, and Crocodylus moreletii. For Nahá, the three species of most importance are Basiliscus vittatus, Boa imperator, and Kinosternon leucostomum. The differenceslie in the fact that for the Lacandones of Metzabok, the most important animals are those that are represented in their oral narratives, while for the Nahá community; the most important species are those that they usually find on a daily basis when walking along the trails in the jungle.

Identification of novel genera and subcluster classifications for mycobacteriophages.

Aim: To identify novel genera amongst mycobacteriophages (MP) and verify a hypothesised correlation between the taxonomy set by the International Committee on Taxonomy of Viruses (ICTV) and the National Centre for Biotechnology Information (NCBI) with that of the Actinobacteriophage Database, which may help formalise subcluster assignment. Methods: A dataset of 721 MP genomes was analysed using VIRIDIC, a nucleotide alignment-based software that predicts genus assignments. Potentially novel genera were analysed using Gegenees and VICTOR, respectively. These genera were then compared to the subclusters assigned by the Actinobacteriophage Database to verify a hypothesis that one genus can be assigned to one subcluster (i.e., the genus-subcluster hypothesis). Results: Initially, when comparing the current genus classifications of the 721 MP dataset to the Actinobacteriophage database subcluster assignments, 83.3% of subclusters supported the genus-subcluster hypothesis. Following the sequential VIRIDIC, Gegenees and VICTOR analyses, a total of 20 novel genera were identified based on a ≥ 70% and ~ 50% similarity threshold for VIRIDIC and Gegenees, respectively, and a monophyletic nature in the VICTOR output. Interestingly, these criteria also appear to support the creation of 13 novel subclusters, which would increase the support for the genus-subcluster hypothesis to 97.6%. Conclusion: The link between genus and subcluster classifications appears robust, as most subclusters can be assigned a single genus and vice versa. By relating the taxonomic and clustering classification systems, they can be easily kept up to date to best reflect MP diversity, which could aid the rapid selection of related (or diverse) phages for research, therapeutic and diagnostic purposes.

The anatomic classification of the anophthalmic eye socket (Types 0–V): A high-level taxonomy classification system

Eyelid and orbital deformities caused by various defects, such as tumor resection and trauma, whether congenital or acquired, are extremely complex and atypical. Several classifications systems for these anophthalmic conditions have been developed, but none have proven suitable for determining the ideal reconstructive surgical strategy. We therefore designed a novel system known as the Anatomic Classification of the Anophthalmic Eye Socket (Types 0-V) for optimum reconstruction of anophthalmic socket deformities focusing on eyelid and orbital defects. Type 0 is an eyelid defect type, in which only the eyelid is defective; Type I is a phthisis bulbi type, in which the anatomical eyeball is preserved, but the visual function is lost; Type II is a substitution type involving filling with implant packing after evisceration or enucleation; Type III is an enucleation type involving enucleation of the ophthalmus; Type IV is an exenteration (incomplete) type involving exenteration while saving the eyelids; and Type V is an exenteration (complete) type involving exenteration including eyelid defects. Using this classification system, it will be possible to standardize reconstructive procedures of the anophthalmic socket.

Semi-Detail Soil Survey and Land Suitability Evaluation for Sugarcane Production at Tungan Ahmadu District, Koko-Besse LGA Kebbi State Nigeria

A semi-detailed soil survey and land suitability evaluation for sugarcane production was conducted at Tungan Ahmadu Koko-Besse LGA, of Kebbi State Nigeria to obtain comprehensive soil data for characterization and classification. The aim was to generate detailed information on the properties, genesis, land characteristics, and classification of soils for their suitability for sugarcane production. The study was carried out in a 4,000ha land area. An interval of 250x250m was used for augering and surface sampling of the soils at a scale of 1:25.000. In each soil mapping unit that was identified a soil profile pit was dug, described and soils sampled in each horizon from bottom-up, to minimize contamination by falling debris and was analyzed in the laboratory. Each soil profile pit was dug to a standard size (200 cm long, 100 cm wide, and a maximum depth of 200 cm or until an impenetrable layer or water table was encountered. Each pit was described regarding its full range of morphological characteristics according to International Standard these include soil depth, horizon thickness, the color of matrix and mottles, texture, structure, consistency, porosity, included materials, roots, and horizon boundary. In addition, records of vegetation/land use, slope, depth to the water table, and internal drainage status was obtained for each profile. Measured variables in the data set were analyzed using descriptive statistics such as means and weighted average. Seven soil mapping units tagged TGA1, TGA2, TGA3, TGA4, TGA5, TGA6, and TGA7 were identified based on landforms and soil properties. The soils are slightly acidic (6.30) to moderately acidic (5.60) had low total nitrogen, organic carbon, and CEC hence low fertility. The soils in the study area are moderately deep, poorly drained, and generally loamy sand to sandy in texture. Based on the USDA Soil Taxonomy classification system, three soil units were identified as TGA1, TGA4, TGA5 and TGA6 (Haplustepts), TGA2 and TGA7 (Haplustalfs), and TGA3 (Terriorthents) which correlate according to the World Reference Base (WRB) as Luvisols, Arenosols, and Fluvisols respectively. Analyses on climate, topography, physical soil properties, wetness and fertility suitability at the research site returned results of TGA2, TGA3, TGA4, TGA5 and TGA6, moderately suitable (S2) while TGA1 and TGA7 are marginally suitable (S3) with limited factors of physical and chemical properties.

The 16S rRNA gene and cyanobacterial taxonomy; current problems and future prospects

Research into cyanobacterial diversity dates back to more than 150 years. Advancement in modern molecular, ultrastructural, ecophysiological and in vitro culture techniques broadened our understanding in the cyanobacterial diversity. Molecular data, especially 16S rRNA gene sequence provide basic criteria for present day cyanobacterial taxonomy. As more DNA sequence data become available it came into notice that morphology-based taxonomic classification is unreliable and it could not infer evolutionary relationships. Some strains belonging to the previously assembled taxa which were classified based on traditional morphological distinctness appeared phylogenetically unrelated when their 16S rRNA gene was sequenced. Therefore, this editorial note was written with the objective of highlighting the necessity in revising present system of cyanobacterial classification and importance in establishment of universal criteria for future taxonomic proposals for cyanobacteria. A cyanobacterial phylogenetic tree was reconstructed using past and present 16S rRNA sequence assemblages from the database and from our studies. Phylogenetic tree revealed polyphyletic origin of unicellular order Chroococcales and filamentous order Oscillatoriales. Strains in the genera Pseudanabaena from the present study were phylogenetically more distant from rest of the Oscillatorialeans in the database and may have independently diverged from the common ancestor at an early stage in the evolution. On the other hand, two Leptolyngbya strains from the present study clustered with Leptolyngbya accessions from the database, although two strains shared only 89% sequence identity. It appears that those two strains could be distinct species belong to the genera of Leptolyngbya and each may have independent evolutionary history. This hypothesis was supported by distinct morphological characters shown in axenic cultures. Present study highlight the importance in understanding that molecular data alone could only provide insights into genetic variability and phylogenetic relatedness, but could not recognize phenotypic variability and their ecological importance and ongoing diversification of strains etc. Thus, construction of an accurate taxonomic classification system requires a ‘polyphasic’ approach that combines molecular data with phenotypic, biochemical and ecophysiological data. Also it is necessary to revisit all past assemblages of taxa available in the database in order to avoid future taxonomic mislabelling.

Harmonisation of a large-scale historical database with the actual Czech soil classification system

The possibility of the adequate use of data and maps from historical soil surveys depends, to a large measure, on their harmonisation. Legacy data originating from a large-scale national mapping campaign, “Systematic soil survey of agricultural soils in Czechoslovakia (SSS, 1961–1971)”, were harmonised and converted according to the actual system of soil classification and descriptions used in Czechia – the Czech taxonomic soil classification system (CTSCS). Applying the methods of taxonomic distance and quantitative analysis and reclassification of the selected soil properties, the conversion of two types of mapping soil units with different detailed soil information (General soil representative (GSR), and Basic soil representative (BSR)) to their counterparts in the CTSCS has been effectuated. The results proved the good potential of the used methods for the soil data harmonisation. The closeness of the concepts of the two classifications was shown when a number of soil classes had only one counterpart with a very low taxonomic distance. On the contrary, soils with variable soil properties were approximating several related units. The additional information on the soil skeleton content, texture, depth and parent material, available for the BSR units, showed the potential in the specification of some units, though the harmonisation of the soil texture turned out to problematic due to the different categorisation of soil particles. The validation of the results in the study region showed a good overall accuracy (75% for GSR, 76.1% for BSR) for both spatial soil units, when better performance has been observed in BSR. The conversion accuracy differed significantly in the individual soil units, and ranged from almost 100% in Fluvizems to 0% in Anthropozems. The extreme cases of a complete mis-classification can be attributed to inconsistencies originating in the historical database and maps. The study showed the potential of modern quantitative methods in the legacy data harmonisation and also the necessity of a critical approach to historical databases and maps.

Inventory study of plants collection in the Medicinal Thematic Garden, Cibodas Botanic Gardens

CBG’s plant collection managed and displayed in the garden based on the taxonomic classification system and thematic system. Plant collection that managed as a thematic system displayed and managed as a thematic garden. The aim of this study is to conduct an inventory study of CBG medicinal thematic garden collections and to do a literature study about the potential medicinal use of plant collection in CBG medicinal thematic gardens. Data collected through surveyed, checked and validated in the information system of CBG plants data collection from CBG Registration Unit. Recorded medicinal use of surveyed plant collection was identified by the literature study. Data were analyzed descriptively. The result of the study showed that there were 26 species from 23 genera and 22 families of medicinal plant species in CBG medicinal thematic garden. Based on ICD-10-WHO, CBG medicinal plant collections can treat 14 ICD-10-WHO diseases. From these 14 diseases, eight diseases can be treated by five CBG medicinal plant collections. These species were utilized as a medicinal plant by using part of the plant (root, leaves, bark, flowers, fruit, seeds, sap) or the whole plant through pounded or boiled processing, and mixed it with other ingredients.

The e-Flora of South Africa – restructuring data to comply with Darwin Core standards for inclusion into the World Flora Online

The e-Flora of South Africa project was initiated in 2013 by the South African National Biodiversity Institute (SANBI) in support of the Global Strategy for Plant Conservation (GSPC, 2011-2020). South Africa's flora consists of ca. 21,000 taxa of which more than half are endemic. South Africa will contribute a national Flora towards Target 1 of the GSPC ("To create an online flora of all known plants by 2020"). South Africa's contribution is ca. 6% of the world’s flora of which ca. 3% are endemic and therefore unique. South Africa’s electronic Flora is comprised of previously published descriptions. South Africa’s e-Flora data forms part of the Botanical Dataset of Southern Africa (BODATSA) that is currently managed through the Botanical Research And Herbarium Management System (BRAHMS). To date, South Africa’s e-Flora data (http://ipt.sanbi.org.za/iptsanbi/resource?r=flora_descriptions) represents 19,539 indigenous taxa, 79,139 descriptions of distribution, morphological, habitat and diagnostic data, and 27,799 bibliographic records. The e-Flora data was recently published online using the Integrated Publishing Toolkit and henceforth harvested by the World Flora Online (WFO) into the portal. A series of challenges were encountered while manipulating descriptive data from BRAHMS to be ingested by the WFO portal; from taxonomic issues to data quality issues not excluding compliance to data standards. To contribute to the WFO portal, the taxa in BODATSA has to match with the taxa in the WFO taxonomic backbone. Once there is a match, a unique WFO taxon identifier is assigned to the taxa in BODATSA. This process presented various challenges because the WFO taxonomic backbone and the taxonomic classification system that is used by South Africa (South African National Plant Checklist) does not fully correlate. The schema used to store taxonomic data also does not agree between BRAHMS and WFO and had to be addressed. To enable consistency for future, a detailed guideline document was created providing all the steps and actions that should be taken when publishing an e-Flora, managed in BRAHMS, to the WFO portal. The presentation will focus on matching taxonomic classifications between BRAHMS and WFO; dealing with character encoding issues and manipulating data to meet Darwin Core standards.

Comparision of fertility capability and taxonomic classification systems to classify the soil map units in some parts of Chaharmahal-va-Bakhtiari province

Although fertility capability classification (FCC) has high performance in land evaluation and soil maps interpretation, so far it has been less attended in land evaluation studies. Therefore, qualitative (FCC method) and quantitative (Riquer index) land fertility capability evaluation for Wheat and Rice cultivation and comparison of Soil Taxonomy and WRB classification with FCC were chosen as this study objective. After field and laboratory studies, the soil map was prepared with the scale of 1: 50,000. Then, FCC and Riquer methods were used to determine the land fertility capability for Wheat and Rice cultivation for each of the soil map unites. Investigations showed that the FCC and Riquer methods have presented similar results and well interpreted and classified soils. The results of Riquer method indicated that the fertility capability of these lands is good except in gravelly and shallow parts, thus Wheat and Rice can be cultivated in these soils. A comparison of the current soil classification systems and the FCC results showed that the problems and inherent characteristics of studied soils were pointed well by the FCC system, whereas they have been expressed differently in Soil Taxonomy and WRB classifications. Gleyic condition, dryness and subsoil gravel are the most limitative factors to Wheat and Rice cultivation in this area.

Genome constitution and evolution of Elytrigia lolioides inferred from Acc1, EF-G, ITS, TrnL-F sequences and GISH

BackgroundElytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of E. lolioides is still unknown. To identify the genome constitution and evolution of E. lolioides, we used single-copy nuclear genes acetyl-CoA carboxylase (Acc1) and elongation factor G (EF-G), multi-copy nuclear gene internal transcribed space (ITS), chloroplast gene trnL-F together with fluorescence and genomic in situ hybridization.ResultsDespite the widespread homogenization of ITS sequences, two distinct lineages (genera Pseudoroegneria and Hordeum) were identified. Acc1 and EF-G sequences suggested that in addition to Pseudoroegneria and Hordeum, unknown genome was the third potential donor of E. lolioides. Data from chloroplast DNA showed that Pseudoroegneria is the maternal donor of E. lolioides. Data from specific FISH marker for St genome indicated that E. lolioides has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of Hordeum genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of Acc1 sequences was detected in E. lolioides possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6–26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH.ConclusionsPhylogenetic and in situ hybridization indicated the presence of two sets of Pseudoroegneria and one set of Hordeum genome in E. lolioides. The genome formula of E. lolioides was designed as StStStStHH. E. lolioides may have originated through the hybridization between tetraploid Elymus (StH) and diploid Pseudoroegneria species. E and unknown genomes may participate in the speciation of E. lolioides through introgression. According to the genome classification system, E. lolioides should be transferred into Elymus L. and renamed as Elymus lolioidus (Kar. er Kir.) Meld.

Building geochemically based quantitative analogies from soil classification systems using different compositional datasets.

Soil heterogeneity is a major contributor to the uncertainty in near-surface biogeochemical modeling. We sought to overcome this limitation by exploring the development of a new classification analogy concept for transcribing the largely qualitative criteria in the pedomorphologically based, soil taxonomic classification systems to quantitative physicochemical descriptions. We collected soil horizons classified under the Alfisols taxonomic Order in the U.S. National Resource Conservation Service (NRCS) soil classification system and quantified their properties via physical and chemical characterizations. Using multivariate statistical modeling modified for compositional data analysis (CoDA), we developed quantitative analogies by partitioning the characterization data up into three different compositions: Water-extracted (WE), Mehlich-III extracted (ME), and particle-size distribution (PSD) compositions. Afterwards, statistical tests were performed to determine the level of discrimination at different taxonomic and location-specific designations. The analogies showed different abilities to discriminate among the samples. Overall, analogies made up from the WE composition more accurately classified the samples than the other compositions, particularly at the Great Group and thermal regime designations. This work points to the potential to quantitatively discriminate taxonomically different soil types characterized by varying compositional datasets.

Deriving Candidate List of Korean Native Organisms for Ecotoxicity Testing: (1) Aquatic Test Species

Ecotoxicity data for ecological risk assessment were obtained according to test conditions presented in international standard test methods. However, only 25.8% of native organisms in Korea were included in international standard test methods. It is needed to consider native organisms in Korea as test species, in terms of toxicity sensitivity, domestic environment media, and economic costs. In this study, we collected taxonomic classification system (Kingdom animalia, plantae, protista), based on Phylum or Division and Class. We investigated the habitat and analyzed the presence or absence of international standard test methods and Korean native organisms. As for animalia, 26 of Class was derived from the fresh water as habitat. Eight and three of Class were derived from the each criteria ’not included in standard test methods and identifiable Korean native organisms’ and ’not included in Korean native organisms in standard test methods and identifiable Korean native organisms’. With Korean native species list, taxonomic and ecological status, distribution, toxicity data, we verified the possibility of list for potential Korean native organisms (eleven of Class). This study proposes the candidate list of Korean native organisms to further develope ecotoxicity testing. Key words: Domestic Species, Ecotoxicity, Aquatic Toxicity, Native Organisms

Chemical weathering indices applied to soils developed on old lake sediments in a semi-arid region of Turkey

Climate is a major influence on weathering processes affecting soil parent materials. Important contributors to soil formation in arid and semi-arid climatic zones are the diurnal cycles of solar heating and cooling that cause mechanical or physical disintegration of rock or parent materials, and wind-blown sands that score and abrade exposed rock surfaces. By using the Soil Taxonomy classification system, the initial aim of this study was to carry out a pedological evaluation for four soil profiles, classified as Xeric Haplocalcid and Xeric Haplocambid, formed on different parent materials (limestone, marl and old alluvial deposits) under the same conditions, including topography and vegetation, in a semiarid region. The second stage was the exploration of the similarities and differences in the classifications resulting from either the pedogenic processes, or from other factors, by determining the degree of soil weathering using geochemical data. To achieve this, soil samples were collected from the horizons to investigate their mineralogical, geochemical and physiochemical properties. The study also considered other features, such as the pedogenic evolution of soils, through the use of weathering indices, namely the Chemical Index of Alteration (CIA), Chemical Index of Weathering (CIW), Base/R2O3 Ratio, Weathering Index of Parker (WIP) and Plagioclase Index of Alteration (PIA). The results clearly showed that soil development at the Altınova State Farm at Konya in the Central Anatolia region of Turkey is due to slow pr ogressive weathering. For this case, the main indicators are secondary calcium carbonate illuviation and weak structural development with a weathering ratio of silicon to aluminium greater than two in all profiles.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

Regionalización Físico-Geográfica (RFG) de Jalisco, México a escala 1:500, 000


 
 
 El proceso de Regionalización físico-geográfica (RFG), es una forma de clasificación del espacio geográfico en unidades homo- géneas. La diferenciación de las unidades se realiza teniendo en cuenta índices diagnósticos, según el sistema de clasificación taxonómica propuesto para México (Bollo et al., 2015), en el cual se diferencia al territorio de estudio en las unidades inferiores de la clasificación: Subprovincias, Distritos y Regiones físico-geográficas. De tal manera, el proceso de regionalización de los pai- sajes físico-geográficos del estado de Jalisco, permitió la distinción y delimitación a detalle de, 15 Subprovincias, 28 Distritos y 66 Regiones físico-geográficas. Las unidades espaciales obtenidas pueden ser utilizadas en estudios regionales de la degradación ambiental, en diagnósticos del estado del medio ambiente del territorio, y como unidades ambientales para distintas formas de ordenamiento del territorio, entre otras aplicaciones. 
 
 

A System-Theoretic Accident Model and Process with Human Factors Analysis and Classification System taxonomy

Formal methods are necessary for effective analysis of the causes of complex accidents. One of possibilities is the System-Theoretic Accident Model and Processes (STAMP) using a hierarchical safety control structure for finding control flaws leading to hazards. The aim of this paper is to enhance STAMP error taxonomy by Human Factors Analysis and Classification System (HFACS). The method proposed in this paper is STAMP-HFACS framework for accident analysis. This framework is STAMP structure-driven, i.e. levels of the HFACS structure are incorporated into components of the STAMP safety control structure. A result of the proposed procedure is the STAMP-HFACS diagram. To illustrate the applicability of the method one thread of the Überlingen midair accident was analyzed. The STAMP-HFACS methodology can express interactions between people, technical equipment, and the environment. It is not bound to an incident/accident events chain. It allows for an analysis of a safety-related occurrence focused on finding some adverse relationships between the components, especially at higher levels of the HFACS methodology. Proper recognition of these relationships, and especially their interpretation in system-theoretic terms related to specific components, can be of great importance for increasing the level of air traffic safety.

Copyright and the Use of Images as Biodiversity Data

Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document the attributes (characters) of organisms, with emphasis on those can be used to distinguish species from each other. Character information is compiled in the scientific literature as text, tables, and images. The information is presented according to conventions that vary among taxonomic domains; such conventions facilitate comparison among similar species, even when descriptions are published by different authors.There is considerable uncertainty within the taxonomic community as to how to re-use images that were included in taxonomic publications, especially in regard to whether copyright applies. This article deals with the principles and application of copyright law, database protection, and protection against unfair competition, as applied to images. We conclude that copyright does not apply to most images in taxonomic literature because they are presented in a standardized way and lack the individuality that is required to qualify as ‘copyrightable works’. There are exceptions, such as wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes (such as visual art). Further exceptions may apply to collections of images that qualify as a database in the sense of European database protection law. In a few European countries, there is legal protection for photographs that do not qualify as works in the usual sense of copyright. It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration. In observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.

Phylogeny of non‐monophyletic Teucrium (Lamiaceae: Ajugoideae): Implications for character evolution and taxonomy

AbstractTeucrium, with an almost cosmopolitan distribution, comprises about 250 species and is the second ‐ largest genus of subfamily Ajugoideae (Lamiaceae). Phylogenetic studies were conducted using nuclear ribosomal DNA (ITS) and chloroplast (ndhF gene, trnL‐F region) DNA sequence data from 101 taxa to estimate phylogenetic relationships among Teucrium and its closest allies. We conclude that: (1) Teucridium, Spartothamnella and Oncinocalyx are nested within Teucrium, thus rendering the latter paraphyletic; (2) previously proposed taxonomic classification systems for Teucrium mostly are not supported by our phylogenetic results; (3) Rubiteucris and Schnabelia appear to be sister to Teucrium. Our results indicate that, among various morphological characters, the calyx shape is diagnostic for different clades within Teucrium. Based on the cladograms derived in this study, the pattern of karyotype evolution suggests that switches in ploidy level are common in at least two groups. Adaptations to drought stress and the regional establishment of Mediterranean climates obviously facilitated speciation and the spread of the genus. Molecular dating analyses indicate diversification of Teucrium at the middle/late Miocene boundary, correlated with Tertiary climatic and tectonic changes.

Emerging trends and a comet taxonomy based on the volatile chemistry measured in thirty comets with high-resolution infrared spectroscopy between 1997 and 2013

A systematic analysis of the mixing ratios with respect to H2O for eight species (CH3OH, HCN, NH3, H2CO, C2H2, C2H6, CH4, and CO) measured with high-resolution infrared spectroscopy in thirty comets between 1997 and 2013 is presented. Some trends are beginning to emerge when mixing ratios in individual comets are compared to average mixing ratios obtained for all species within the population. The variation in mixing ratios for all measured species is at least an order of magnitude. Overall, Jupiter-family comets are depleted in volatile species with respect to H2O compared to long-period Oort cloud comets, with the most volatile species showing the greatest relative depletion. There is a high positive correlation between the mixing ratios of HCN, C2H6, and CH4, whereas NH3, H2CO, and C2H2 are moderately correlated with each other but generally uncorrelated or show only weak correlation with other species. CO is generally uncorrelated with the other measured species possibly because it has the highest volatility and is therefore more susceptible to thermal evolutionary effects. Most of these correlations appear to be independent of dynamical class with a few possible exceptions. Molecular mixing ratios for CH3OH, HCN, C2H6, and CH4 show an expected behavior with heliocentric distance suggesting a dominant ice source, whereas there is emerging evidence that the mixing ratios of NH3, H2CO, C2H2, NH2, and CN may increase at small heliocentric distances, suggesting the possibility of additional sources related to the thermal decomposition of organic dust. Although this provides information on the composition of the most volatile grains in comets, it presents an additional difficulty in classifying comet chemistry because most comets within this dataset were only observed over a limited range of heliocentric distance. Although there is remarkable compositional diversity resulting in a unique chemical fingerprint for each comet, a hierarchical tree cluster analysis is used to determine a taxonomic classification system containing four groups and eleven subgroups. Optical and infrared comparisons indicate that mixing ratios of daughter species and potential parents from cometary ices are sometimes but not always consistent with one another. This suggests that in many comets there are significant sources of C2 and/or CN from grains, and that the importance of these sources is variable within the comet population.

The Ancient Evolutionary History of Polyomaviruses.

Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.