Current Taxonomic Classification Research Articles

Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis

Many molecular phylogenies of viruses build upon the analysis of single genes. The study of whole-genomes, however, might yield more reliable information to infer tree topologies and a better approach for drawing the evolutionary history of virus families. In this study, we apply a novel comparative proteomic approach to seek whether incorporating information from the entire proteome would support the actual taxonomy of the family Bromoviridae. Our results suggest that the current taxonomic classification should be modified in several aspects to account for the genomic properties of the Bromoviridae. These differences are: i) Alfalfa mosaic virus (AMV) is a true Ilarvirus instead of constituting an independent genus; ii) Pelargonium zonate spot virus (PZSV) should be considered as a member of the Bromoviridae; and iii) the genus Ilarvirus should be divided into fewer phylogenetic subgroups than suggested by antigenic differences.

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.

Molecular identification of pathogenic house dust mites using 12S rRNA sequences

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.

Taxonomic and Chemical Relationships Revealed by Nuclear Magnetic Resonance Spectra of Plant Exudates

Exudates collected from 65 species of gymnosperms and angiosperms were examined by solid-state carbon-13 (13C) nuclear magnetic resonance (NMR) spectroscopy. Diagnostic criteria were developed to distinguish resins, gums, and gum resins. The typology generated from the exudate spectra generally follows current taxonomic classifications, suggesting that 13C NMR spectroscopy may have applications in exudate identification, at least at the familial level, and in some cases at the generic or specific levels.

Sesquiterpene lactone-based classification of three Asteraceae tribes: a study based on self-organizing neural networks applied to chemosystematics

This work describes an application of artificial neural networks on a small data set of sesquiterpene lactones (STLs) of three tribes of the family Asteraceae. Structurally different types of representative STLs from seven subtribes of the tribes Eupatorieae, Heliantheae and Vernonieae were selected as input data for self-organizing neural networks. Encoding the 3D molecular structures of STLs and their projection onto Kohonen maps allowed the classification of Asteraceae into tribes and subtribes. This approach allowed the evaluation of structural similarities among different sets of 3D structures of sesquiterpene lactones and their correlation with the current taxonomic classification of the family. Predictions of the occurrence of STLs from a plant species according to the taxa they belong to were also performed by the networks. The methodology used in this work can be applied to chemosystematic or chemotaxonomic studies of Asteraceae.

Behavior of Pigment Cells Closely Correlates the Manner of Gastrulation in Sea Urchin Embryos

To know whether behavior of pigment cells correlates the process of gastrulation or not, gastrulating embryos of several species of regular echinoids (Anthocidaris crassispina, Mespilia globulus and Toxopneustes pileolus) and irregular echinoids (Clypeaster japonicus and Astriclypeus manni) were examined. In M. globulus and A. crassispina, the archenteron elongated stepwise like in well-known sea urchins. In the embryos of both species, fluorescent pigment cells left the archenteron tip and migrated into the blastocoel during gastrulation. In T. pileolus, C. japonicus and A. manni, on the other hand, the archenteron elongated at a constant rate throughout gastrulation. In these species, no pigment cell was observed at the archenteron tip during invagination processes; pigment cells began to migrate in the ectoderm from the vegetal pole side toward the apical plate without entering the blastocoel. These results clearly indicate that the behavior of pigment cells closely correlated the manner of gastrulation. Further, it was examined whether the archenteron cells are rearranged during invagination, by comparing the number of cells observed on cross sections of the archenteron at the early and late gastrula stages. The rearrangement was not conspicuous in A. crassispina and M. globulus, in which archenteron elongated stepwise. In contrast, the archenteron cells were remarkably rearranged in C. japonicus, alothough the archenteron elongated continuously. Thus, neither the behavior of pigment cells nor the manner of gastrulation matches the current taxonomic classification of echinoids.

Morphological Studies toward an Improved Classification of Campanulaceae s. str.

Growth and seedling morphology of 144 species representing 30 genera of Campanulaceae s. str. were studied. Two types of seedlings were found: Group A, with an elongated epicotyl and elongated internodes, and Group B, with a shortened (not visible) epicotyl and usually shortened internodes. These two types appear to be correlated with other vegetative characters. Thus, plants from Group A have an opposite leaf arrangement (at least early in ontogenesis), rhythmic seasonal growth with a long dormant period, and sympodial branching. Plants from Group B have a spiral leaf arrangement, continuous growth (at least in the non-flowering period), and sympodial and monopodial branching. Taxa in Group A are distributed mostly in Asia, whereas representatives in Group B occur almost worldwide. The two groups do not coincide with current taxonomic classifications but correspond remarkably well with the distribution of other characters such as pollen-grain morphology and correlate with groups based on molecular analysis; therefore, these two groups may reflect two lineages. Growth and seedling morphology are of taxonomic significance in Campanulaceae and can be used for treatments in conjunction with other characters. Taxonomic changes, which are supported by molecular data, are proposed.

Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data

Oak gallwasps are cyclically parthenogenetic insects that induce a wide diversity of highly complex species- and generation-specific galls on oaks and other Fagaceae. Phylogenetic relationships within oak gallwasps remain to be established, while sexual and parthenogenetic generations of many species remain unpaired. Previous work on oak gallwasps has revealed substantial intra-specific variation, particularly between regions known to represent discrete Pleistocene glacial refuges. Here we use statistical phylogenetic inference methods on sequence data for a fragment of the mitochondrial cytochrome b gene to reconstruct the relationships among 62 oak gallwasp species. For 16 of these we also include 23 additional cytochrome b haplotype sequences from different Pleistocene refuge areas to test the effect of intra-specific variation on inter-specific phylogeny reconstruction. The reconstructed phylogenies show good intra-generic resolution and identify several conserved clades, but fail to reconstruct either very recent or very ancient divergences. Nine of the 16 species represented by multiple haplotypes are not monophyletic. The apparent discordance between the recovered gene tree and the current taxonomic classification can be explained through: (a) collapsing of some species currently known only from either a sexual or a parthenogenetic generation into a single cyclically parthenogenetic entity; (b) sorting of ancestral polymorphism in diverging lineages, and (c) horizontal transfer of haplotypes, perhaps due to hybridization within glacial refuges. Our conclusions emphasise the need for careful intra-specific sampling when reconstructing phylogenies for radiations of closely related species and imply that for certain taxonomic groups full phylogenetic resolution (using molecular markers) may not be attainable.

Patterns in Fluorescence over a Caribbean Reef Slope: the Coral Genus Madracis

Patterns of fluorescence and colony tissue, colour were studied (field observations and epifluorescence microscopy) in six species of the coral genus Madracis over depth from 10 to 60 m at a reef slope in Curaçao. Two functions showed up: (1) Decrease in number of colourmorphs (n = 25) with depth suggests a photo-protective function where short wavelengths (e.g. UV) are transformed to long wavelengths, (2) Green fluorescence, observed in four species over their entire depth range, transforms radiation to wavelengths useful for photosynthesis. The observed patterns in fluorescence between species did not correspond to the current taxonomic classification. Our results do not support the usefulness of fluorescence as a taxonomic tool in corals.

Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae).

Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C. The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42%), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct G+C contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

Microsporogenesis, microgametogenesis and pollen morphology of Passiflora spp. (Passifloraceae)

Microsporogenesis, microgametogenesis and pollen morphology of six species of genus Passiflora L. belonging to three subgenera (Passiflora, Dysosmia, Decaloba) were studied with light and scanning microscopy; P. caerulea was also examined with transmission microscopy. The tapetum is secretory, microspore tetrads are tetrahedral and pollen grains are two-celled when shed. Small Ubisch bodies are attached to a peritapetal membrane; they are a product of tapetal activity and the rough endoplasmic reticulum (ERr) appears to be involved in their origin. The pollen grains of all the species are subspheroidal, zonocolpate, geminicolpate. Each pair of colpi anastomoses at the poles. The exine is semitectate, reticulate, heterobrochate. The muri are simplibaculate, wavy. The lumina have clavate bacula of varying height. The colpus structure is similar to that of the lumina but generally with fewer and smaller bacula. Lumina size and amount of bacula inside the lumina vary between subgenera. The grains from subgenera Passiflora and Dysosmia differ from those of Decaloba in their size and number of colpi. The pollen and microsporangium morphology of the species of subgenera Passiflora and Dysosmia are more similar than those of subgenus Decaloba. The results are discussed in relation to the current taxonomic classification.

Phylogeny of green sulfur bacteria on the basis of gene sequences of 16S rRNA and of the Fenna-Matthews-Olson protein

The phylogeny of green sulfur bacteria was studied on the basis of gene sequences of the 16S rRNA and of the Fenna-Matthews-Olson (FMO) protein. Representative and type strains (31 strains total) of most of the known species were analyzed. On the basis of fmoA gene sequences from Chlorobium tepidum ATCC 49652(T) and Chlorobium limicola DSM 249(T) available from the EMBL database, primers were constructed that allowed sequence analysis of a major part of the fmoAgene. The largely congruent phylogenetic relationship of sequences of the fmoA gene and of 16S rDNA gives considerable support to the phylogeny of green sulfur bacteria previously suggested on the basis of 16S rDNA sequences. Distinct groups of strains were recognized on the basis of 16S rDNA and FMO sequences and supported by characteristic signature amino acids of FMO. Marine strains formed clusters separate from freshwater strains. The resulting phylogenetic grouping and relationship of the green sulfur bacteria do not correlate with their current taxonomic classification.

An investigation of genetic variation in Banksia integrifolia (Proteaceae) by the use of the AFLP technique

The Banksia integrifolia L.f. species complex has undergone several taxonomic treatments over the past 20 years. In order to gain further insight into phenetic relationships between the taxa of this species, the distribution of genetic variation over the geographic range of B. integrifolia was investigated by the amplified fragment length polymorphism (AFLP) technique. Ordination and classification analyses resulted in clusters of individuals that closely conformed to the different taxa of this species. Further ordination and classification analyses of individuals of just B. integrifolia subsp. integrifolia indicate that there are also geographical patterns within the subspecies, with those individuals from the north of the species’ range clustering away from those in the south of the range. A Mantel-test between morphological data collected in a previous study and molecular data collected in this study indicated a highly significant correlation between morphological and genetic variation. This study thus supports the current taxonomic classification of the B. integrifolia species complex.

Phylogenetic Relationships within the Eared Seals (Otariidae: Carnivora): Implications for the Historical Biogeography of the Family

Phylogenetic relationships within the family Otariidae were investigated using two regions of the mitochondrial genome. A 360-bp region of the cytochrome b gene was employed for the primary phylogenetic analysis, while a 356-bp segment of the control region was used to enhance resolution of the terminal nodes. Traditional classification of the family into the subfamilies Arctocephalinae (fur seals) and Otariinae (sea lions) is not supported, with the fur seal Callorhinus ursinus having a basal relationship relative to the rest of the family. This is consistent with the fossil record which suggests that this genus diverged from the line leading to the remaining fur seals and sea lions about 6 million years ago (mya). There is also little evidence to support or refute the monophyly of sea lions. Four sea lion clades and five fur seal clades were observed, but relationships among these clades are unclear. Similar genetic divergences between the sea lion clades (Da = 0.054–0.078), as well as between the major Arctocephalus fur seal clades (Da = 0.040–0.069) suggest that these groups underwent periods of rapid radiation at about the time they diverged from each other. Rapid radiations of this type make the resolution of relationships between the resulting species difficult and indicate the requirement for additional molecular data from both nuclear and mitochondrial genes. The phylogenetic relationships within the family and the genetic distances among some taxa highlight inconsistencies in the current taxonomic classification of the family.

Microarray-based survey of repetitive genomic sequences in Vicia spp.

A modified DNA microarray-based technique was devised for preliminary screening of short fragment genomic DNA libraries from three Vicia species (V. melanops, V. narbonensis, and V. sativa) to isolate representative highly abundant DNA sequences that show different distribution patterns among related legume species. The microarrays were sequentially hybridized with labeled genomic DNAs of thirteen Vicia and seven other Fabaceae species and scored for hybridization signals of individual clones. The clones were then assigned to one of the following groups characterized by hybridization to: (1) all tested species, (2) most of the Vicia and Pisum species, (3) only a few Vicia species, and (4) preferentially a single Vicia species. Several clones from each group, 65 in total, were sequenced. All Group I clones were identified as rDNA genes or fragments of chloroplast genome, whereas the majority of Group II clones showed significant homologies to retroelement sequences. Clones in Groups III and IV contained novel dispersed repeats with copy numbers 10(2)-10(6)/1C and two genus-specific tandem repeats. One of these belongs to the VicTR-B repeat family, and the other clone (S12) contains an amplified portion of the rDNA intergenic spacer. In situ hybridization using V. sativa metaphase chromosomes revealed the presence of the S12 sequences not only within rDNA genes, but also at several additional loci. The newly identified repeats, as well as the retroelement-like sequences, were characterized with respect to their abundance within individual genomes. Correlations between the repeat distributions and the current taxonomic classification of these species are discussed.

Species differentiation of North American spruce (Picea) based on morphological and anatomical characteristics of needles

Differentiation of most North American spruce (Picea) species can be done based on needle morphology and anatomy. Picea breweriana S. Watson, Picea chihuahuana Martìnez, Picea mariana (Mill.) BSP, Picea martinezii Patterson, and Picea rubens Sarg. needles have two continuous resin ducts extending from near the base to near the tip. Picea engelmannii Parry ex Engelm., Picea glauca (Moench) Voss, Picea pungens Engelm., Picea mexicana Martìnez, and Picea sitchensis (Bong.) Carr. needles have variable numbers of short, intermittent resin ducts or sacs. Within each of these groups, most species could be differentiated based on cross-sectional shape, resin-duct diameter, and resin-duct position. Picea mariana and P. rubens, and P. glauca and P. engelmannii are two pairs with similar needles, but they can be differentiated using linear discriminant analysis based on resin-duct diameter and position in cross section. Paleoecological and paleoclimatological studies may be facilitated by species-level identification of plant macrofossils because of different ecological adaptations of each species. Resin-duct continuity patterns are generally consistent with current taxonomic classifications, except for P. glauca. Based on our results, together with DNA and crossing studies, P. glauca is apparently more closely related to P. engelmannii and P. sitchensis than to P. rubens and P. mariana, with which it is often classified. Picea pungens is probably more distantly related to P. engelmannii than has been assumed in some previous classifications. Picea martinezii and P. chihuahuana may be very closely related to each other.Key words: spruce, Picea, North America, needle, resin duct, anatomy.

Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms.

The current taxonomic classification of Chlamydia is based on limited phenotypic, morphologic and genetic criteria. This classification does not take into account recent analysis of the ribosomal operon or recently identified obligately intracellular organisms that have a chlamydia-like developmental cycle of replication. Neither does it provide a systematic rationale for identifying new strains. In this study, phylogenetic analyses of the 16S and 23S rRNA genes are presented with corroborating genetic and phenotypic information to show that the order Chlamydiales contains at least four distinct groups at the family level and that within the Chlamydiaceae are two distinct lineages which branch into nine separate clusters. In this report a reclassification of the order Chlamydiales and its current taxa is proposed. This proposal retains currently known strains with > 90% 16S rRNA identity in the family Chlamydiaceae and separates other chlamydia-like organisms that have 80-90% 16S rRNA relatedness to the Chlamydiaceae into new families. Chlamydiae that were previously described as 'Candidatus Parachlamydia acanthamoebae' Amann, Springer, Schönhuber, Ludwig, Schmid, Müller and Michel 1997, become members of Parachlamydiaceae fam. nov., Parachlamydia acanthamoebae gen. nov., sp. now. 'Simkania' strain Z becomes the founding member of Simkaniaceae fam. nov., Simkania negevensis gen. nov., sp. nov. The fourth group, which includes strain WSU 86-1044, was left unnamed. The Chlamydiaceae, which currently has only the genus Chlamydia, is divided into two genera, Chlamydia and Chlamydophila gen. nov. Two new species, Chlamydia muridarum sp. nov. and Chlamydia suis sp. nov., join Chlamydia trachomatis in the emended genus Chlamydia. Chlamydophila gen. nov. assimilates the current species, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia psittaci, to form Chlamydophila pecorum comb. nov., Chlamydophila pneumoniae comb. nov. and Chlamydophila psittaci comb. nov. Three new Chlamydophila species are derived from Chlamydia psittaci: Chlamydophila abortus gen. nov., sp. nov., Chlamydophila caviae gen. nov., sp. nov. and Chlamydophila felis gen. nov., sp. nov. Emended descriptions for the order Chlamydiales and for the family Chlamydiaceae are provided. These families, genera and species are readily distinguished by analysis of signature sequences in the 16S and 23S ribosomal genes.

An estimate of phylogenetic relationships among culicine mosquitoes using a restriction map of the rDNA cistron.

Restriction maps of the rDNA cistron of twelve species of mosquitoes in six genera of the subfamily Culicinae were constructed using eight 6 bp recognition restriction enzymes. Anopheles albimanus was used as an outgroup. The size of the rDNA cistron ranged from 8.5 kb in Aedes katherinensis to 12.9 kb in Ae. polynesiensis. A total of twenty-six sites were scored; eighteen were polymorphic among ingroup taxa. The proportion of polymorphic nucleotide sites (Pnuc) was 0.059 and the heterozygosity per nucleotide site (Hnuc) was 0.028. Wagner and Fitch Parsimony, Dollo Parsimony and Nei-Li distance/neighbour-joining methods were used to construct phylogenetic trees. The rDNA RFLP dataset did not provide a well-supported phylogeny among culicine taxa. The RFLP phylogenies are incongruent with the morphology character based and molecular phylogenies and derived relationships did not correspond with current taxonomic classifications. The lack of resolution was due to homoplasy arising from frequent independent loss or gain of restriction sites among unrelated taxa.

Genetic Variation among Populations of River Otters in North America: Considerations for Reintroduction Projects

Horizontal starch gel electrophoresis was used to assess variability at 23 presumptive gene loci of 732 river otters obtained from fur-trappers in 18 states and three Canadian provinces. States and provinces providing otters were sorted into eight geographic regions for genetic comparisons. Multilocus heterozygosity and polymorphism ranged from 0.018 to 0.032 and 0.044 to 0.087, respectively. One locus, esterase-2, (EST-2) demonstrated a high level of polymorphism throughout all regions. Malate dehydrogenase-1 (MDH-1) was polymorphic throughout the Mississippi drainage but not elsewhere. Heterozygosity, occurrence of rare alleles, and mean number of alleles per locus were associated positively with estimated population sizes. Average heterozygosity and polymorphism values for otters within regions were lower than overall averages reported for mammals but similar to the range of those observed in other mammalian carnivores. Patterns of gene flow suggested by the distribution of polymorphism at the MDH-1 locus do not concur with the current taxonomic classification of river otters. Levels of genetic variation detected in this investigation present a positive outlook for the maintenance of genetic diversity in river otter populations, if sound management principles are applied for reintroductions.

ITS sequences from nuclear rDNA suggest unexpected phylogenetic relationships between Euro-Mediterranean, East Asiatic and North American taxa ofQuercus (Fagaceae)

Nucleotide sequences from the internal transcribed spacer (ITS) regions of the 18S–26S nuclear ribosomal DNA have been studied from ten species ofQuercus (representing four subgenera),Castanea sativa andFagus sylvatica, as a preliminary molecular contribution to the still poorly understood systematics and evolution ofFagaceae. The resulting matrix has been used to calculate pair-wise sequence divergence indices and to construct a maximum parsimony tree forQuercus coding indels as a fifth state. Divergence is greater forQuercus vs.Fagus than forQuercus vs.Castanea. The tree for theQuercus taxa studied reveals two clearly divergent clades. In clade I the evergreen W MediterraneanQ. suber appears in a basal position as sister to more distal deciduous taxa, i.e. the E MediterraneanQ. macrolepis and the E AsiaticQ. acutissima (all formerly united as different sections under the apparently polyphyletic subg.Cerris), andQ. rubra (a representative of the N American subg.Erythrobalanus), forming a pair withQ. acutissima. In clade II the evergreen southeastern N AmericanQ. virginiana is basal and sister to the remaining three branches, i.e. a pair of evergreen Mediterranean taxa withQ. ilex andQ. coccifera (subg.Sclerophyllodrys), the deciduous but otherwise plesiomorphic SE European/SW AsiaticQ. cerris (type species of subg.Cerris), and the related but more apomorphic European pairQ. petraea andQ. robur (subg.Quercus). These results partly conflict with current taxonomic classification but are supported by some anatomical and morphological characters. They document polyphyletic lines from evergreen to deciduous taxa and suggest Tertiary transcontinental connections within the genus.