Large Taxonomic Groups Research Articles

Identification of mealybug pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach

Pseudococcidae (mealybugs) is a large taxonomic group, including a number of agronomic pests. Taxonomic identification of mealybug species is a recurrent problem and represents a major barrier to the establishment of adequate pest management strategies. We combined molecular analysis of three DNA markers (28S-D2, cytochrome oxidase I and internal transcribed spacer 2) with morphological examination, for the identification of 176 specimens collected from 40 mealybug populations infesting various crops and ornamental plants in Egypt and France. This combination of DNA and morphological analyses led to the identification of 17 species: seven in Egypt (Planococcus citri (Risso), Planococcus ficus (Signoret), Maconellicoccus hirsutus (Green), Ferrisia virgata (Cockerell), Phenacoccus solenopsis Tinsley, Phenacoccus parvus Morrison and Saccharicoccus sacchari (Cockerell)) and 11 in France (Planococcus citri, Pseudococcus viburni Signoret, Pseudococcus longispinus (Targioni-Tozzetti), Pseudococcus comstocki (Kuwana), Rhizoecus amorphophalli Betrem, Trionymus bambusae (Green), Balanococcus diminutus (Leonardi), Phenacoccus madeirensis Green, Planococcus vovae (Nasonov), Dysmicoccus brevipes (Cockerell) and Phenacoccus aceris Signoret), Pl. citri being found in both countries. We also found genetic variation between populations considered to belong to the same species, justifying further investigation of the possible occurrence of complexes of cryptic taxa.

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

BackgroundPopulation levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups.ResultsGene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups.ConclusionsProbe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

Density-Dependent Phase Polyphenism in Nonmodel Locusts: A Minireview

Although the specific mechanisms of locust phase transformation are wellunderstood for model locust species such as the desert locustSchistocerca gregariaand the migratory locustLocusta migratoria, the expressions of density-dependent phase polyphenism in other nonmodel locust species are not wellknown. The present paper is an attempt to review and synthesize what we know about these nonmodel locusts. Based on all available data, I find that locust phase polyphenism is expressed in many different ways in different locust species and identify a pattern that locust species often belong to large taxonomic groups which contain mostly nonswarming grasshopper species. Although locust phase polyphenism has evolved multiple times within Acrididae, I argue that its evolution should be studied from a phylogenetic perspective because I find similar density-dependent phenotypic plasticity among closely related species. Finally, I emphasize the importance of comparative analyses in understanding the evolution of locust phase and propose a phylogeny-based research framework.

Limb bone allometry during postnatal ontogeny in non‐avian dinosaurs

Although the interspecific scaling of tetrapods is well understood, remarkably little work has been done on the ontogenetic scaling within tetrapod species, whether fossil or recent. Here the ontogenetic allometry of the femur, humerus, and tibia was determined for 23 species of non-avian dinosaur by regressing log-transformed length against log-transformed circumference for each bone using reduced major axis bivariate regression. The femora of large theropod species became more robust during ontogeny, whereas growth in the femora of sauropodomorphs and most ornithischians was not significantly different from isometry. Hadrosaur hindlimb elements became significantly more gracile during ontogeny. Scaling constants were higher in all theropods than in any non-theropod taxa. Such clear taxonomically correlated divisions were not evident in the ontogenetic allometry of the tibia and hindlimb bones did not scale uniformly within larger taxonomic groups. For taxa in which the ontogenetic allometry of the humerus was studied, only Riojasaurus incertus exhibited a significant departure from isometry. Using independent contrasts, the regression of femoral allometry against the log of adult body mass was found to have a significant negative correlation but such a relationship could not be established for other limb elements or growth parameters, mainly due to the small sample size. The intraspecific scaling patterns observed in dinosaurs and other amniotes do not support earlier hypotheses that intraspecific scaling differs between endothermic and ectothermic taxa.

A Generic Impact‐Scoring System Applied to Alien Mammals in Europe

We present a generic scoring system that compares the impact of alien species among members of large taxonomic groups. This scoring can be used to identify the most harmful alien species so that conservation measures to ameliorate their negative effects can be prioritized. For all alien mammals in Europe, we assessed impact reports as completely as possible. Impact was classified as either environmental or economic. We subdivided each of these categories into five subcategories (environmental: impact through competition, predation, hybridization, transmission of disease, and herbivory; economic: impact on agriculture, livestock, forestry, human health, and infrastructure). We assigned all impact reports to one of these 10 categories. All categories had impact scores that ranged from zero (minimal) to five (maximal possible impact at a location). We summed all impact scores for a species to calculate "potential impact" scores. We obtained "actual impact" scores by multiplying potential impact scores by the percentage of area occupied by the respective species in Europe. Finally, we correlated species' ecological traits with the derived impact scores. Alien mammals from the orders Rodentia, Artiodactyla, and Carnivora caused the highest impact. In particular, the brown rat (Rattus norvegicus), muskrat (Ondathra zibethicus), and sika deer (Cervus nippon) had the highest overall scores. Species with a high potential environmental impact also had a strong potential economic impact. Potential impact also correlated with the distribution of a species in Europe. Ecological flexibility (measured as number of different habitats a species occupies) was strongly related to impact. The scoring system was robust to uncertainty in knowledge of impact and could be adjusted with weight scores to account for specific value systems of particular stakeholder groups (e.g., agronomists or environmentalists). Finally, the scoring system is easily applicable and adaptable to other taxonomic groups.

Developmental and tissue-specific expression of NITRs

Novel immune-type receptors (NITRs) are encoded by large multi-gene families and share structural and signaling similarities to mammalian natural killer receptors (NKRs). NITRs have been identified in multiple bony fish species, including zebrafish, and may be restricted to this large taxonomic group. Thirty-nine NITR genes that can be classified into 14 families are encoded on zebrafish chromosomes 7 and 14. Herein, we demonstrate the expression of multiple NITR genes in the zebrafish ovary and during embryogenesis. All 14 families of zebrafish NITRs are expressed in hematopoietic kidney, spleen and intestine as are immunoglobulin and T cell antigen receptors. Furthermore, all 14 families of NITRs are shown to be expressed in the lymphocyte lineage, but not in the myeloid lineage, consistent with the hypothesis that NITRs function as NKRs. Sequence analyses of NITR amplicons identify known alleles and reveal additional alleles within the nitr1, nitr2, nitr3, and nitr5 families, reflecting the recent evolution of this gene family.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-009-0416-5) contains supplementary material, which is available to authorized users.

ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies

Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified ∼4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR’s taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries.Database URL: http://www.orionbiosciences.com/research/orion-vircat.html

Evolution of the Apicomplexa: where are we now?

The Apicomplexa is the only large taxonomic group whose members are entirely parasitic and is, therefore, presumably of major interest to parasitologists. We might, for example, expect that we know a great deal about the biology of the group by now and that we have a clear phylogenetic framework within which to organize that knowledge. It might thus come as a surprise to learn that in terms of biodiversity, the Apicomplexa is actually the least-known group of all. Furthermore, the taxonomic framework for the Apicomplexa is rather tenuous in many respects. This situation is unlikely to change in the short term.

How many loci does it take to DNA barcode a crocus?

BackgroundDNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.Methodology and Principal FindingsHere we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will – as is the case in crocus – undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached – even in a taxonomic context.Conclusions/SignificanceThe time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.

Sex difference in life span affected by female birth rate in modern humans

Sex differences in life span are common in different taxa, including primates, but not well understood. Theory and comparative evidence suggest that differential costs of reproduction between the sexes may explain the differences in sex-biased mortality across large taxonomic groups. The level of sex-specific reproductive effort may thus affect the difference in life span across populations. Modern humans ( Homo sapiens), generally show the typical mammalian pattern of male-biased mortality. Here, I asked whether the differences in female birth rates between countries affect the sex difference in life span. I used the data on male and female life span and female birth rate in different countries from publicly available databases, while controlling for geographic and economic factors. The analysis suggests that female birth rate explains 17% of the variation in relative sex differences in life span across countries. Low female birth rate results in females living relatively longer than males. These data suggest that a simple biological factor—female birth rate—may explain a significant part of the variation in sex differences in life span across human populations.

A TEST OF REPRODUCTIVE POWER IN SNAKES

Reproductive power is a contentious concept among ecologists, and the model has been criticized on theoretical and empirical grounds. Despite these criticisms, the model has successfully predicted the modal (optimal) size in three large taxonomic groups and the shape of the body size distribution in two of these groups. We tested the reproductive power model on snakes, a group that differs markedly in physiology, foraging ecology, and body shape from the endothermic groups upon which the model was derived. Using detailed field data from the published literature, snake-specific constants associated with reproductive power were determined using allometric relationships of energy invested annually in egg production and population productivity. The resultant model accurately predicted the mode and left side of the size distribution for snakes but failed to predict the right side of that distribution. If the model correctly describes what is possible in snakes, observed size diversity is limited, especially in the largest size classes.

Cytogenetics studies in thirteen Brazilian species of Phaneropterinae (Orthoptera: Tettigonioidea: Tettigoniidae): main evolutive trends based on their karyological traits

The thirteen species of Phaneropterinae here studied can be arranged in four different groups according to their basic karyological traits. All of them share the same kind of chromosomal sex determining mechanism with X0 (male sign) and XX(female sign). The X chromosome differs among species and always appears heteropycnotic during prophase I, it is the largest in the set and segregates precociously during anaphase I. Among the species, the karyotypes varies in fundamental number between 31 to 21. The meaning of these significant changes in the karyotypes in relation to the phylogeny within some large taxonomic group of species is discussed.

Microbes Colonize a Baby’s Gut with Distinction

Microbes Colonize a Baby’s Gut with Distinction

TaxMan: a taxonomic database manager.

BackgroundPhylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes) can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study.ResultsTaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level) and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy.ConclusionTaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of both annotation and BLAST similarity, it ensures that all available sequence data can be brought to bear on a phylogenetic problem, but remains fast enough to cope with many thousands of records. By automatically assisting in the selection of the best subset of taxa to address a particular phylogenetic problem, TaxMan greatly speeds up the process of generating multiple sequence alignments for phylogenetic analysis. Our results indicate that an automated phylogenetic workbench can be a useful tool when correctly guided by user knowledge.

Taxonomy and Conservation: A Case Study from Chamaedorea alternans

The establishment of justified recommendations in conservation biology requires robust taxonomic treatments for the group(s) being considered. Controversial or poorly developed taxonomies can have a negative impact on conservation assessments. One example of a taxonomically difficult and controversial species complex that is important in conservation involves two species of Mexican palms, Chamaedorea tepejilote and C. alternans. The goal of this study was to investigate whether C. alternans and C. tepejilote are genetically distinct within the Los Tuxtlas region of Veracruz. Individuals corresponding to the morphology of C. alternans and C. tepejilote were collected from sympatric and allopatric regions within the Los Tuxtlas Biological Station. Eighty-eight samples were genotyped using amplified fragment length polymorphism (AFLP) markers. Cluster and ordination analyses were used to investigate patterns of differentiation. UPGMA and PCO analyses of AFLP profiles recovered two divergent clusters corresponding to morphologically defined C. tepejilote and C. alternans. No intermediate genotypes were observed and five of the 45 loci were fixed for either the presence or absence between the species. The patterns of divergence observed do not identify a role for sympatric speciation. The observed patterns of differentiation support the recognition of C. alternans as distinct from C. tepejilote. A suite of vegetative and reproductive morphological features can be used to help distinguish these taxa in the field, but they can be difficult to differentiate from preserved material. Previous treatments of the variation found within the complex (C. alternans and C. tepejilote) as intraspecific variance is unjustified. Given that the Los Tuxtlas region has suffered from historical and ongoing deforestation and that Chamaedorea includes numerous endangered taxa, retaining conservation status for C. alternans serves to help safeguard individuals of the species as well as a region and larger taxonomic group all under considerable threat from human activities.

Regional versus Climatic Effect on Taxon Richness in Angiosperms: Reply to Qian and Ricklefs

Taxonomic richness varies strikingly over global spatial scales. Equally striking are the strong correlations between these broad-scale patterns of richness and climate. The number of species, genera, or families in broad taxonomic or functional groups that occur in quadrats spread over broad areas (continents to the globe as a whole) co-varies with temperature and/or water availability (or related variables) with coefficients of determination typically between 70% and 90% (Wright et al. 1993; Hawkins et al. 2003b). Richness-climate relationships have been documented for terrestrial plants (Currie and Paquin 1987; Adams and Woodward 1989; O’Brien 1993), terrestrial vertebrates (Turner et al. 1988; Currie 1991), insects (Turner et al. 1987; Kerr et al. 1998), aquatic invertebrates (Patalas 1990), freshwater fish (Guegan et al. 1998), human pathogens (Guernier et al. 2004), corals (Fraser and Currie 1996), and other taxa. Although these correlations suggest that contemporary climate somehow controls taxonomic richness, perhaps through an intermediary variable such as primary productivity (see Wright et al. 1993 for elaboration of the mechanism), it is possible that richness-climate correlations may be due to collinearity between climate and other unobserved variables that influence richness. Because the climatic hypothesis makes a number of other strong predictions, it can be tested further. The climate hypothesis predicts that similar relationships should be observed in essentially any large taxonomic group, which has been observed (as cited above). The climate hypothesis predicts

Descending neurons of the suprapharyngeal ganglion of a dragonfly Aeschna larvae

Opioid peptides have been revealed in representatives of practically all large taxonomic groups of invertebrates, and the opiate receptors are found even in unicellulars. The opioid system seems to belong to the evolutionary ancient signal systems. The comparative data indicate that the most conservative and ancient function of opioids is control of the adequate level of protective reactions. In the infusorian Stentor the opiate ligands suppress a contractile response to mechanical stimulation, i.e., the protective behavior. In all studies multicellular invertebrates, agonists also suppress protective behavior, whereas antagonists produce opposite effects. This initially signal meaning of opioids might have become a basis for divergent development of their functions in evolution. Already in higher invertebrates, molluscs and arthropods, many functions of opioids, for example, stress-induced analgesia, regulation of feeding and mating behavior, of social aggression, are similar to those in vertebrates. It is suggested that the main events in formation of functions of the endogenous opioid system have occurred in the lower invertebrates that have remained so far the least studied.

Macroecologia de mamíferos neotropicais com ocorrência no Cerrado

The macroecological approach has been used recently to analyze correlations between ecological variables in large taxonomic groups, at continental scales. A positive relationship between body weight and geographic range size has been described as a poligonal space envelope form, that can be explained by ecological and evolutionary constraints. However, these variables can be disturbed by spatial and phylogenetic autocorrelation effects. In this work, the relationship between body weight and geographic range size was analyzed for 80 species of Neotropical mammals present in the Brazilian cerrado. Spatial and taxonomic effects were tested using a linear trend surface analysis and an ANOVA (at level of order), combined in a generalized model. Around 61% of variation in geographic range size and 69% of variation in body weight in mammals of the cerrado can be explained simultaneously by spatial and taxonomic effects. The analysis of residuals of the generalized model showed that positive correlation between variables persist even after removing these effects. Thus, variation and covariation of traits in the mammals of the brazilian cerrado agree with the general macroecological pattern proposed for another taxonomic groups such as mammals, birds and snakes worldwilde.

Cloning and functional expression of a cDNA encoding a pheromone gland-specific acyl-CoA Delta11-desaturase of the cabbage looper moth, Trichoplusia ni.

Desaturation of coenzyme-A esters of saturated fatty acids is a common feature of sex pheromone biosynthetic pathways in the Lepidoptera. The enzymes that catalyze this step share several biochemical properties with the ubiquitous acyl-CoA Delta9-desaturases of animals and fungi, suggesting a common ancestral origin. Unlike metabolic acyl-CoA Delta9-desaturases, pheromone desaturases have evolved unusual regio- and stereoselective activities that contribute to the remarkable diversity of chemical structures used as pheromones in this large taxonomic group. In this report, we describe the isolation of a cDNA encoding a pheromone gland desaturase from the cabbage looper moth, Trichoplusia ni, a species in which all unsaturated pheromone products are produced via a Delta11Z-desaturation mechanism. The largest ORF of the approximately 1,250-bp cDNA encodes a 349-aa apoprotein (PDesat-Tn Delta11Z) with a predicted molecular mass of 40,240 Da. Its hydrophobicity profile is similar overall to those of rat and yeast Delta9-desaturases, suggesting conserved transmembrane topology. A 182-aa core domain delimited by conserved histidine-rich motifs implicated in iron-binding and catalysis has 72 and 58% similarity (including conservative substitutions) to acyl-CoA Delta9Z-desaturases of rat and yeast, respectively. Northern blot analysis revealed an approximately 1,250-nt PDesat-Tn Delta11Z mRNA that is consistent with the spatial and temporal distribution of Delta11-desaturase enzyme activity. Genetic transformation of a desaturase-deficient strain of the yeast Saccharomyces cerevisiae with an expression plasmid encoding PDesat-Tn Delta11Z resulted in complementation of the strain's fatty acid auxotrophy and the production of Delta11Z-unsaturated fatty acids.

A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution.

We complied a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.