The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics.     

Scanning electron microscopy of cultures of rare macromycetous fungi

Using scanning electron microscopy it was possible to describe structures on the mycelia of macromycetous fungi that possess both taxonomic and functional importance. For taxonomic characteristization of 11 studied species, the presence and distribution of clamps on hyphæ represent an, important feature; in the case ofLyophyllum decastes the form of clamps may be useful for identifying cultures. Formation and types of anamorhps inPleurotus calyptratus, Montagnea arenaria andLyophyllum decastes are also of taxonomic importance. For additional taxonomic characterization of cultures ofTricholoma mongolicum the formation of “coils” might be exploited. Formation of anastomoses and crystals has predominantly a physiological role. However, in our view, production of crystals under certain culture conditions may serve as a diagnostic parameter.     

Taxonomic chauvinism revisited: insight from parental care research

Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001–2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article—specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines— in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an ‘ornithological Mafia’ conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future work.     

Phenotypes of Phosphoglucose isomerase,phosphoglucose mutase and general protein in some freshwater molluscs from Basrah,Iraq

Electrophoretic variants of phosphoglucose isomerase (EC.5.3.1.9) and phosphoglucose mutase (EC.2.7.5.1) have been studied in eight species of freshwater molluscs. Two phenotypes of phosphoglucose isomerase were observed in Melanopsis nodosa and one phenotype was observed in the rest of the species. One phenotype of phosphoglucose mutase was observed in all the species of molluscs studied. Phosphoglucose isomerase is inferred to be a dimer encoded at a single polymorphic locus in Melanoides nodosa. There are two alleles at this locus. Phosphoglucose mutase is inferred to be a monomer encoded at a single monomorphic locus in all species. The electrophoretic analysis revealed that phosphoglucose isomerase enzyme cannot be considered a good taxonomic criterion to differentiate the different members of the six families studied but, on the other hand, it is considered a good taxonomic criterion to differentiate Melanopsis nodosa and Theodoxus jordani. Phosphoglucose mutase is considered a good taxonomic criterion to differentiate the family Melanidae from the remaining five families studied. General protein can be considered a good taxonomic criterion to differentiate the family Corbicullidae from Melanidae, Viviparidae and Neritidae but, on the other hand, it seems to be a less useful taxonomic criterion to differentiate between the Viviparidae and Neritidae.     

Ant taxonomic and functional beta-diversity respond differently to changes in forest cover and spatial distance

Habitat change affects both taxonomic and functional biodiversity, and beta-diversity is often used as a metric to describe these changes. Furthermore, spatially closer communities tend to have more similar species compositions (lower beta-diversity). These changes in community composition can be revealed with taxonomic and functional aspects of diversity. We assessed the responses of ant taxonomic and functional beta-diversity to changes in forest cover and spatial distance. We expected that changes in taxonomic and functional beta-diversity along a forest cover gradient would be caused by the replacement of open-habitat ant species by forest-habitat ant species. We sampled ants within twelve landscapes with different forest cover percentages in the southwestern Amazon of Brazil. Both taxonomic and functional beta-diversity of pairwise samples (β_BC) were partitioned into their turnover (β_Bal) and nestedness (β_Gra) components. Increasing forest cover correlated with increases in taxonomic and functional β_BC, however, β_Bal had a greater contribution to taxonomic β_BC and β_Gra to functional β_BC. Taxonomic β_BC and β_Bal and functional β_Bal increased with spatial distance. Forest-habitat species richness increased, and open-habitat species richness decreased with increasing forest cover, while the richness of habitat-use generalist species did not vary. The loss of environmental heterogeneity may be responsible for generalist species dominance and open-habitat species presence in less-forested landscapes. This leads to great taxonomic replacement, but a nestedness gradient of function. Better land use planning is needed to ensure biodiversity and ecosystem functions of forest habitats in human-modified landscapes.     

Changes in the taxonomic diversity of the reef fish community of San José Island, Gulf of California, Mexico

Although San José Island is considered one of the most important islands in the lower Gulf of California due to its commercial fishing activities, few studies have evaluated their fish taxonomic diversity. The aim of this study was to determine the variation in the taxonomic diversity of the conspicuous fish community in eight locations around San José Island from March 2001 to February 2002. We assessed the changes in the diversity of rocky reef fish based on the taxonomic distances between species, using Fisher’s alpha diversity index, average taxonomic distinctiveness (AvTD Δ+), and taxonomic distinctiveness (Δ*). Visual censuses were conducted in 48 transects consisting of 100?×?5?m quadrants (500?m² sampling area) at an average depth of 5?m, from 09:00 to 16:00. A total of 26,608 fishes belonging to 112 species and 76 genera were found. The index of relative abundance was used to determine the most important species, which were in order of abundance: Abudefduf troschelii, Thalassoma lucasanum, Stegastes rectifraenum, Mulloidichthys dentatus, Chromis atrilobata, Lutjanus argentiventris, and Scarus ghobban. According to Fisher’s alpha diversity index, the highest diversity of species was found in July and the lowest in February. The indices of Δ+ and Δ* indicated significant temporal and spatial differences.     

Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions

Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.     

Floristic summary ofManual of Vascular Plants of Northeastern United States and Adjacent Canada,second edition

The second edition of theManual of Vascular Plants of Northeastern United States and Adjacent Canada by Gleason and Cronquist (1991) is the most recent and up-to-date taxonomic treatment of the flora of that region. Since no floristic summary of theManual was included in the publication, a computer analysis of the taxonomic data of theManual was performed in order to generate a floristic summary. Totals of 4285 species, 1091 genera, and 191 families were tabulated. The largest genus wasCarex, with 230 species; the largest family was the Asteraceae, with 528 species. Comparisons made with earlier floras of the same region indicated small declines on the order of 10% for these taxonomic groups.     

Comparison of the epifauna spatial distribution in Posidonia oceanica,Cymodocea nodosa and unvegetated bottoms: Importance of meadow edges

In order to detect the influence of seagrass, the most important habitats of shallow soft-bottom along the Mediterranean coast, on spatial distribution of epifauna, four different types of habitat were sampled: Posidonia oceanica, Cymodocea nodosa, edge of Posidonia meadow and sandy bottoms. Sampling was carried out, using the hand net method, in various random sites and at different times (April 95, August 95 and February 96) on the Alicante coast (SE Spain). A double taxonomic approach was used in order to detect spatial and temporal changes in the abundance of the main taxonomic groups and amphipod species. The differences among habitats were detected by non-parametric multidimensional scaling (MDS) for community structure and by analysis of variance for groups and amphipod populations. The community structure defined by the abundance of taxonomic groups was not significantly modified by the habitats. Single abundance of taxonomic groups also had no significant preference for the type of habitat except in the case of Acari, a group linked to Posidonia. However, certain trends of preference, such as mysids on Posidonia edge and isopods on Cymodocea, were detectable. On other hand, the amphipod assemblage showed important differences among habitats. Some species changed significantly in abundance depending on the habitat considered, e.g. Dexamine spiniventris and Perioculodes longimanus. It was possible to conclude that there is an important influence of Posidonia and Cymodocea on epifauna distribution by diversification of habitat structure on sandy bottoms, but it was more important at the species level than when considering taxonomic groups. Furthermore, sandy bottoms and the meadow edges had a relatively high importance on fauna distribution, depending on taxa and the period of the year.     

Para-aminophenylalanine in vigna: Possible taxonomic and ecological significance as a seed defence against bruchids

Seeds of eight wild species and varieties from Vigna subgenera Plectotropis and Vigna were screened for the non-protein amino acid p-aminophenylalanine (PAPA), previously reported to have a restricted taxonomic distribution and to be a growth inhibitor of Escherichia coli. The compound was detected in five wild species and its distribution found to have taxonomic value for assessing members of Plectotropis and intrageneric links with other taxa. Although quantitative variation in PAPA was detected between species and also between varieties of V. vexillata, toxicity tests confirmed that the levels detected in all accessions were sufficient for PAPA to be an important component of resistance against two important pest bruchids of Vigna and Phaseolus crops. The taxonomic and ecological significance of these findings is discussed.     

The effect of shade on petiole length in the viola fimbriatula-sagittata complex (Violaceae)

In many taxonomic treatments, Viola fimbriatula is distinguished from V. sagittata by the length of the petiole. Field experiments, using both cloned plants and plants grown from seed, demonstrated considerable phenotypic plasticity in petiole length. Neither relative nor absolute petiole length furnishes a useful taxonomic distinction here.     

Identifying functional species pool of planktonic protozoa for discriminating water quality status in marine ecosystems

It is cost-effective protocol to identify a functional species pool for marine bioassessment by removing redundant species from a raw dataset. The feasibility of functional species pool for discriminating water quality status was studied based on a dataset of 120 samples of ciliated protozoa. From the full 60-species dataset of the whole ciliate communities, a 35-species subset was identified as a functional species pool, the species number, abundance and biodiversity indices of which were significantly correlated with those of the full species dataset. The spatial pattern of the subset was significantly related to the changes in nutrients soluble reactive phosphates (SRP), nitrate/nitrite nitrogen (NO₃-N/NO₂-N) and ammonium nitrogen (NH₄-N). Four indices of the taxonomic diversity (Δ), taxonomic distinctness (Δ*), average in taxonomic distinctness (Δ⁺) and the variation in taxonomic distinctness (Λ⁺) based on this small species pool were significantly correlated with the changes of nutrients NO₃-N and/or (NH₄-N). The paired indices Δ⁺ and Λ⁺ showed a clear decreasing trend of departure from the expected taxonomic pattern. These findings suggest that the 35-species functional species subset may be used as a feasible functional surrogate of ciliated protozoan assemblages for community-based bioassessment in marine ecosystems.     

Cecropia telenitida Cuatrec. (Urticaceae: Cecropieae): Phytochemical diversity,chemophenetic implications and new records from Central America

The Neotropical genus Cecropia is the largest genus of Cecropieae in the Urticaceae family with 61 described species. For many years, the taxonomic study of Cecropia has been based on morphological and anatomical data. However, recent studies have shown that chemical entities present in Cecropia can be used to establish differences between species providing important additional support on its taxonomic classification. The goal of the present study was to contribute to the phytotaxonomic knowledge of this genus to better inform taxonomic decisions. In addition, this is the first time that chemical constituents have been described in the leaves of Cecropia telenitida Cuatrec., a species that until now had not been reported in Central America. We characterized and quantified the polyphenolic composition of the methanol leaf extract of C. telenitida using UPLC-DAD-MS and HPLC-DAD, respectively. Phytochemical analysis showed that this extract was rich in chlorogenic acid and flavone C-glycosides, with isoorientin and isoorientin 2″-O-xyloside as the main compounds. Our data showed a lower chemical diversity and metabolite concentrations than other related species. Morphological, distributional and taxonomic notes, images of the plant and phytochemical comparisons between C. telenitida and selected congeners from Panama are also provided.     

Systematic variation in amino acid compositions of grass caryopses

Variation in amino acid patterns of 121 species (72 genera) of grass caryopses is extensively consistent with taxonomic groupings. The patterns of pooids and chloridoids are distinguishable from one another and from those of eu-panicoids and andropogonoids; the bamboos, Oryza, Stipeae, Ehrharta and Microlaena, which share certain morphological and anatomical features, also share a characteristic amino acid profile, while profiles of danthonoioids, Triodia and Aristida are clearly non-pooid. Caryopsis amino acid patterns vary independently of photosynthetic pathway. Embryos from taxonomically diverse genera all show very similar amino acid profiles, which differ strikingly from those of the endosperms, and the amino acid patterns of whole caryopses are dominated by their endosperms, which are responsible for the taxonomic variation. ‘Chemical scores’ of the caryopsis proteins, but not total protein contents, correlate to some extent with taxonomic groupings.     

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.     

The use of an oligonucleotide that hybridizes to DNA sequences interspersed in the genome of members of the genusPhytophthora as an adjunct to morphological criteria in species identification

An oligonucleotide (primer), designed from a conserved region of the multi-allelicb locus of the basidiomycete fungusUstilago maydis, generated reproducible PCR fingerprints inPhytophthora species. The primer hybridized in a species-specific manner to nucleotide sequences interspersed in the genome of the closely related members ofPhytophthora taxonomic group IV. We recommend the use of this PCR procedure as an alternative method for resolving the close taxonomic affinity of some members of the genusPhytophthora.     

Taxonomy and ecological niche modeling: Implications for the conservation of wood partridges (genus Dendrortyx)

Ecological niche models (ENMs) have a wide range of biological applications, particularly in conservation. To build these models, two sources of information are needed: occurrence records for the species of interest and environmental variables. However, taxonomic limits are often unclear, and the selection of occurrence data depends on the species concept being used. In this study we generated ENMs based on different taxonomic levels within the Dendrortyx group, which is comprised of three species and several subspecies; we analyzed the geographic and ecological distribution patterns and discuss the implications for the biogeography and conservation of this group. Our results suggest that the area with suitable climate depends on the taxonomic category used in the model, which in turn affects the interpretation of the importance of different biogeographic barriers and introduces variation into the potential differentiation of Dendrortyx. In terms of conservation, Dendrortyx macroura and Dendrortyx leucophrys are in a low risk category, that of “least concern,” although they may be amended to a higher category when their allopatric lineages are considered as the units for modeling. We suggest carrying out an a priori taxonomic analysis to facilitate the empirical identification of the units to be modeled in order to allow for a better ecological and biogeographic interpretation and more sound conservation policies.