Ordinal Groups Research Articles

Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations

In placental mammals and birds, molecular data generally support a view that they diverged into their ordinal groups in good response to mid-Cretaceous continental fragmentations. However, such divergence patterns have rarely been studied for reptiles for which phylogenetic relationships among their major groups have not yet been established molecularly. Here, I determined complete or nearly complete mitochondrial DNA sequences from seven lizard families and reconstructed phylogenetic relationships between major lizard families. When snakes were included, maximum likelihood analysis did not support a morphological view of the snakes–varanoids affinity, although several other competing hypotheses on the position of snakes still cannot be discriminated presumably due to extremely long branches of the snake lineages. I also conducted clock-free Bayesian analyses to show that divergence times between major lizard families were centered in Triassic–Jurassic times. Thus, lizards include much deeper divergences than the mammals and birds and they appear to have already radiated into various families prior to the mid-Cretaceous major continental fragmentation.

Measuring and estimating diagnostic accuracy when there are three ordinal diagnostic groups

This article studies the problem of measuring and estimating the diagnostic accuracy when there are three ordinal diagnostic groups. We use a receiver operating characteristic (ROC) surface to describe the probabilities of correct classifications into three diagnostic groups based on various sets of diagnostic thresholds of a test and propose to use the entire and the partial volume under the surface to measure the diagnostic accuracy. Mathematical properties and probabilistic interpretations of the proposed measure of diagnostic accuracy are discussed. Under the assumption of normal distributions of the diagnostic test from three diagnostic groups, we present the maximum likelihood estimate to the volume under the ROC surface and give the asymptotic variance to the estimate. We further propose several asymptotic confidence interval estimates to the volume under the ROC surface. The performance of these confidence interval estimates is evaluated in terms of attaining the nominal coverage probability based on a simulation study. In addition, we develop a method of sample size determination to achieve an adequate accuracy of the confidence interval estimate. Finally, we demonstrate the proposed methodology by applying it to the clinical diagnosis of early stage Alzheimer's disease based on the neuropsychological database of the Washington University Alzheimer's Disease Research Center.

Effect of fire retardant application on heathland surface-dwelling invertebrate communities in Victoria

Summary The effects of the application of fire retardant at varying rates on surface-dwelling invertebrates at ordinal and sub-ordinal level in heathland communities were assessed over a one-year period from March 2001 to March 2002. The study was conducted at two sites, one in East Gippsland at Mario and the other in the Grampians region of south-western Victoria where a total of 136 190 specimens representing 30 ordinal and sub-ordinal taxa contained in 5400 pitfall trap samples was collected. It was concluded that despite the application of fire retardant at varying rates, there was no significant effect on invertebrate activity at ground level amongst the ordinal groups Acarina and Dermaptera. These ordinal groups appear to form a stable component of the heathland invertebrate community at both sites. Although significant changes were observed in other major taxonomic groups (total taxa, total insects, total non-insects, Araneae, Collembola, Coleoptera and Diptera) these changes were confined to either increased or decreased activity within a single plot and were judged to be not representative of treatment. While a significant change in activity was recorded for Formicidae at both sites, this was also due to single-plot variations in activity across different treatments. Such information indicates that any significant changes observed in invertebrate activity appeared to be due to site-related environmental factors rather than the effects of the retardant itself. When assessed in terms of general diversity, taxon richness and community evenness, ordinal and sub-ordinal taxa were unaffected by retardant application at the Mario site. Significant changes in insect diversity at the Grampians site were again due to site-related factors rather than retardant effects. Further study is required to determine whether this stability is reflected at family, genus and species level, and if there are any seasonal and longer-term effects of retardant application. The combined effect of fire and retardant on invertebrate communities also requires further study.

144 Use of Fourier Transform Infrared (FT IR) Diffuse Reflectance Spectroscopy and Hamming Distances to Study the Phycocolloid Chemosystematics of the Red Algae (Rhodophta)

The use of red algal polysaccharide cell wall structures as taxonomic indicators has been a recurring theme in the literature for over 58 years. Traditionally the polymeric phycocolloids of the red algal cell walls have been classified into definite structures (carrageenans and agars) based on the phycocolloids present. However, this method has some obvious shortcomings, such as its inability to assign hybrid structures (carragars), or the appearance of agarocolloids in traditional ‘carrageenophytes’. Thus, there is a need to develop an unbiased method of examining phycocolloid structures without assigning them names. Fourier transform infrared diffuse reflectance spectroscopy was used to analyze the spectra of a large number of red algal species, belonging to several orders. The spectra for each species resulted in a series of ‘peaks’ corresponding to certain wavenumbers (cm−1), which in term correspond to phycocolloid bonds. On the basis of shared/similar peaks, irrespective of their combinations to describe polymeric units, a series of matrices were developed for each family. These were coded as a 0 and 1, indicating the presence or absence of a peak, respectively. Using the concept of vector addition and Hamming distances, a methodology was formulated for analyzing ordinal and familial level groupings. Initial analysis on 173 species, representing 39 families and 12 orders of the Rhodophyta, proved to be promising. Some results corroborated previous studies, while others proved to be informative and raised the need for further chemosystematic studies. This provides the impetus for continuing to develop this method as a contribution to red algal systematics.

Short and long-term effects of prescribed fires in autumn and spring on surface-active arthropods in dry sclerophyll eucalypt forests of Victoria

The effects of two prescribed low-intensity fires in spring and autumn varying from means of 229–303 kW m −1 within the period 1985–1999 on epigeal invertebrates were assessed. The approximately 14 year study was based on 76,375 arthropod specimens, representing 31 ordinal or lower level taxa contained in 3160 pitfall trap samples from a spring and autumn sites burnt twice and an unburnt reference site within a 46.3 ha area. The study indicates that while there appears nil effect by prescribed fires on the surface-active fauna in the short and long term on spring burnt sites and in the short term on autumn burnt sites, in the longer term (over 13 years) on autumn burnt sites, significant increases in total taxa activity in the 1997/99 period, primarily as a result of increases in activity of the groups total non-insects, Acarina, and Formicidae were observed. Conversely, during the same period, a decrease in activity of the Dermaptera was recorded while the situation for the Collembola and Diptera is less certain as changes in activity occurred on both the autumn burnt and unburnt reference sites. However, as no significant change in activity was observed in the short term (i.e. before and immediately after the first fire) for any of the aforementioned taxa, it cannot be stated for certain that the changes in activity following the second fire are due to fire or non-fire effects. This may apply for the Formicidae, especially following the second fire in 1997/99 when both the average soil temperature and soil dryness index (SDI) were substantially higher than that normally experienced thus possibly stimulating increased ant activity. Also, as the study was conducted to ordinal and sub-ordinal level only, it is uncertain whether the above changes in activity are spread over a range or confined to individual species within ordinal groups. Further study should address this issue.

Depression as a Prognostic Factor for Breast Cancer Mortality

It is unclear if depression or depressive symptoms have an effect on mortality in breast cancer patients. In this population-based, nationwide, retrospective cohort study in Denmark, depression was defined as affective or anxiety disorders that necessitated psychiatric hospital admission. All the affective and anxiety disorders were divided and categorized into five ordinal diagnostic groups. Early-stage (N=10382) and late-stage (N=10211) breast cancer patients were analyzed separately with Cox's regression adjusted for well-documented somatic prognostic variables. The authors used survival analysis of data from three central registers and found that breast cancer patients with depression had a modestly but significantly higher risk of mortality depending on stage of breast cancer and time of depression. The same result was found after censoring unnatural causes of death such as accident, suicide, or homicide.

Presenting Manifestations, Cigarette Smoking, and Detection Bias in Age at Diagnosis of Lung Cancer

PURPOSE: To examine the possible role of detection bias in the association between amount of cigarette smoking and age at diagnosis of lung cancer. The bias can occur because primary lung cancer can often escape detection during life and will be found (if at all) as a “necropsy surprise” unless a diagnostic workup is provoked by such presenting manifestations as hemoptysis and a localized chest lesion. The necropsy surprises will be reduced and the reported rates of pre-mortem incidence will be raised if a cigarette smoking history also acts as a diagnostic incentive. METHODS: This possibility was examined in a case series of 1266 patients whose primary lung cancer had been carefully classified according to diverse features at the time of presentation. For the total case group and for pertinent clinical, anatomic, and demographic subgroups, we then examined the trends for age at diagnosis in relation to amount of cigarette smoking. RESULTS: The overall age at diagnosis (median = 63 years; mean = 61.2) remained essentially similar in five ordinal groups of Tumor, Nodes, Metastases (TNM) and four of five Clinical Severity stages, but had an inverse monotonic gradient in six ordinal groups of customary cigarette smoking [from none to >2 packs per day (ppd)]. Because an earlier age of discovery can be explained by either etiologic or detection-bias roles for heavier smoking, its impact was checked in subgroups with and without diagnostically provocative manifestations. In localized lesions, the smoking-age gradient vanished if suspicious “indicator” symptoms were present, but persisted if they were absent. Regardless of symptoms, the age gradient was strengthened in non-localized cancer lesions where smoking might particularly point to a primary diagnostic source in the lung. CONCLUSIONS: Detection bias may play a distinctive, although often overlooked, role in the work-up decisions that precede and lead to a diagnosis of lung cancer.

Phylogenetic Investigations of the Stephanoberyciformes and Beryciformes, Particularly Whalefishes (Euteleostei: Cetomimidae), Based on Partial 12S rDNA and 16S rDNA Sequences

DNA data were collected from a number of acanthomorph fishes for 12S rDNA (30 sequences) and 16S rDNA (39 sequences) to investigate the phylogenetic relationships of genera within Cetomimidae (whalefishes) and of this family within the Stephanoberyciformes/Beryciformes assemblage. The Cetomimidae are apparently monophyletic. Within the family, species of Gyrinomimus and Cetomimus form a clade but the former genus is paraphyletic with respect to the latter. Cetostoma is sister to Ditropichthys rather than to Gyrinomimus plus Cetomimus as suggested by morphological analyses. Rondeletiidae + Cetomimidae + Barbourisiidae are shown, as expected from morphological analyses, as a monophyletic group in the 12S rDNA analyses, but not in the 16S rDNA or combined analyses, although the shortest trees showing the group require only one extra step in each case. These three families plus Melamphaidae (our sample of Stephanoberyciformes) are not shown as a group in any analysis, with Melamphaidae being sister to Berycidae in the 16S and combined analyses, but dispersed in the 12S analyses. Maximum-parsimony trees without imposed constraints are notably shorter than trees constrained to show ordinal groupings or either of the two main current hypotheses of Stephanoberyciformes/Beryciformes relationships. The length difference is highly significant for most comparisons using either 12S or 16S rDNA sets or their combination, and significant or nearly so for all comparisons. In particular, the Beryciformes is unlikely to be monophyletic. The Holocentridae are included, with high bootstrap and Bremer support, in a clade of non-beryciforms comprising the Gempylidae, Zeidae, and Atheriniformes (the only higher acanthomorphs sampled) and not with other Beryciform families. In these data, the Berycidae are the sister to the Melamphaidae, a stephanoberyciform family.

Systematics of naviculoid diatoms: the interrelationships of some taxa with a stauros

A phylogenetic analysis was conducted on 21 biraphid naviculoid diatom species (from three orders and five families, using 5 protoplast and 21 frustule characters) to test whether the recently described genus Craspedostauros was more closely related to members of the Mastogloiaceae or to other stauros-bearing diatoms. The analysis also tested, and confirmed, the hypothesis that the stauros, as recognized by light microscopy, is a homoplastic character. Whereas partitioned analyses of protoplast and frustule data resolved different parts of the ‘total’ tree, using NONA parsimony analysis of all the data, one tree was obtained. This tree placed Craspedostauros in the mastogloialean clade, rather than near Stauroneis, Staurophora, Haslea or Meuniera. The ordinal and familial groupings suggested by Round and others were also confirmed by the analysis, supported particularly by protoplast and some ultrastructural features.

Systematics of naviculoid diatoms: the interrelationships of some taxa with a stauros

A phylogenetic analysis was conducted on 21 biraphid naviculoid diatom species (from three orders and five families, using 5 protoplast and 21 frustule characters) to test whether the recently described genus Craspedostauros was more closely related to members of the Mastogloiaceae or to other stauros-bearing diatoms. The analysis also tested, and confirmed, the hypothesis that the stauros, as recognized by light microscopy, is a homoplastic character. Whereas partitioned analyses of protoplast and frustule data resolved different parts of the ‘total’ tree, using NONA parsimony analysis of all the data, one tree was obtained. This tree placed Craspedostauros in the mastogloialean clade, rather than near Stauroneis, Staurophora, Haslea or Meuniera. The ordinal and familial groupings suggested by Round and others were also confirmed by the analysis, supported particularly by protoplast and some ultrastructural features.

Phycocolloid chemistry as a taxonomic indicator of phylogeny in the Gigartinales, Rhodophyceae: A review and current developments using Fourier transform infrared diffuse reflectance spectroscopy

The taxonomic significance of the polysaccharide structures of algal cell walls has been underscored several times over the past few decades but has never been pursued systematically. Many changes in red algal systematics and the biochemical analyses of phycocolloids have occured in recent years. The cell-wall composi-tion of representatives of 167 (24.7%) genera and 470 (11.5%) species of red algae has been documented.The method developed by Chopin and Whalen for carrageenan identification by Fourier transform infrared diffuse reflectance spectroscopy is extended to the study of phycocolloids for diverse species in many red algal orders. This paper focuses on the Gigartinales in which representatives of 28 (68.3%) families, 88 (50.6%) genera and 224 (27.9%) species have been analyzed. In light of recent molecular phylogenies, some patterns of distribution of key phycocolloid attributes, corresponding to familial and ordinal level groupings, are emerging; however, more species remain to be analyzed. The well-documented biochemical alternation of generations in the Phyllophoraceae, Petrocelidaceae and Gigartinaceae still holds (with two exceptions), but this pattern was not recorded in other families of Gigartinales.

Phylogenetic Interrelationships and Reductive Evolution in Neotropical Characidiin Fishes (Characiformes, Ostariophysi)

Abstract—Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae. Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships among Elachocharax, Klausewitzia, Odontocharacidium and Microcharacidium . An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non-simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the "presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.

PHYLOGENETIC INTERRELATIONSHIPS AND REDUCTIVE EVOLUTION IN NEOTROPICAL CHARACIDIIN FISHES (CHARACIFORMES, OSTARIOPHYSI).

Abstract- Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae. Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships among Elachocharax, Klausewitzia, Odontocharacidium and Microcharacidium. An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non-simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the "presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.

The distribution of acteoside among angiosperms

The distribution of the phenylpropanoid glycoside acteoside is restricted to a constellation of families which may constitute a natural ordinal grouping. This distribution of acteoside contains many families traditionally clustered in a Scrophulariales-Lamiales complex. It includes Retziaceae, Oleaceae, Stilbaceae, and Hippuridaceae, but excludes Hydrostachyaceae.

Statistical Evaluation of Exposure Assessment Strategies

Abstract It is well known that exposure measurement error or misclassification can bias an epidemiologic risk assessment. Accordingly, it is useful to have methods of assessing the degree of error in exposure assessments. This paper proposes statistical evaluation techniques for two types of exposure assessment strategies: categorization of exposure and estimation of actual personal exposure levels (with particular attention to the latter). Categorization of exposure is generally done in one of the two ways: ordinal but nonquantitative grouping or quantitative exposure intervals. Estimation of actual exposure levels is most often done in the form of job-by-year exposure matrices and somewhat less often by exposure prediction models. The nature of uncertainty inherent with each of these approaches is described. Quantitative estimates of the magnitude of error in an exposure assessment are possible when exposure matrices or prediction models are employed. Three types of statistical approaches are explored f...

Phylogenetic relationships within the order Hadromerida (Porifera, Demospongiae, Tetractinomorpha) as indicated by ribosomal RNA sequence comparisons

Despite advances of recent years no stable higher order classification of the Porifera has yet emerged. We present the first approach to addressing this problem using nucleic acid sequencing. In order to resolve relationships at various taxonomic levels it is necessary to utilize a range of species, genera and families. We have focused on one well defined order of Demospongiae, the Hadromerida, and have used 18 S rRNA sequencing to evaluate relationships between seven species belonging to five genera and four families. One species of the order Dictyoceratida has been included to indicate divergence between orders in two subclasses of the Demospongiae. Existing ordinal and familial groups are confirmed and some rearrangement of genera is indicated following sequence alignment and comparison using parsimony analysis. These data can serve as a baseline for molecular approaches to resolving relationships between other sponge groups.

Analysis of Trends in Proportions with an Ordinally Scaled Determinant

AbstractIn this paper the analysis of several proportions in a comparative study setting is discussed. The case of ordinal grouping variates is considered. F statistics are formulated to test for trend in the proportions over the scored values of the determinant variate. The null chi‐square or F (t square) functions are presented separately for the unstratified and stratified analysis, and in either situation the corresponding functions with angular transformed proportions are also expressed. Generalizations to deal with the parameters in the nonnull range are outlined. Throughout, the intimate relation between the presented statistics and standard methods is pointed out.

Symbolic play and early communication development in hearing-impaired children

This study investigated the relationship between symbolic play and language performance for young hearing-impaired children. Subjects included 20 hearing-impaired youngsters ranging in age from 38 months to 69 months. The children were placed in two ordinal communication groups. Placement in one of the communication levels was dependent upon information concerning the number of spontaneous expressive communication units the child produced. The experimental task consisted of three predetermined play themes in which the child previously displayed functional play. A nonconventional item was then included, and the play behaviors were observed for the occurrence of symbolic play under a spontaneous or modeled condition. The results indicate a significant difference in symbolic play between the two ordinal communication levels. Additionally, there was a strong positive relationship observed between the variables of symbolic play and early communication development.

II. Researches on the structure, organisation, and classification of the fossil reptilia. Part III. On parts of the skeleton of a mammal from triassic rocks of Klipfontein, Fraserberg, South Africa ( Theriodesmus phylarchus , Seeley), illustrating the reptilian inheritance in the mammalian hand

The author describes a slab showing impressions of the fore-limb and some other bones of the skeleton, which indicate a plantigrade animal as large as a wolverine. Its general affinities are with flesh eating types. The humerus approximates to that of Thylacinus. The ulna and radius at their proximal ends are like those of Lemuroids and Carnivores, but the forms of the distal articulations are different. The carpus appears to include three central bones. Part of one of the digits appears to have been lost and renewed. The animal is regarded as a primitive type which cannot be placed in any ordinal group which has been defined.

On the Cranial and Vertebral Characters of the Crocodilian Genus Plesiosuchus , Owen

I n the ‘Preliminary Remarks’ to the palæontology of the Crocodilian Reptiles, Cuvier urges the need of a precise determination of the generic characters, with regard to which he writes, “observations, however novel, lose all their merit, unless they rest on this basis”. He proceeds to exemplify the apophthegm by descriptions which have never been surpassed of new and interesting species of extinct Reptiles, especially Crocodilian, which he shows to have been erroneously referred to other previously defined genera. Cuvier refrained from attaching generic names, distinct from those of his “subgenera” of existing Crocodiles, to the extinct forms of which his keen and careful observations had detected characters since generally admitted to merit such distinction, and of which a contemporary availed himself. The characters which Cuvier defines as forming for the Crocodiles a “very natural genus” are now recognized as defining an ordinal group of the class Reptilia. But of this group he admits and names “Subgenera,” and to their distinctive characters he devotes special “Sections,” as, for example, “I°, Espèces de Caymans” (p. 30); “II°, Espèces de Crocodiles” (p. 42); “III°, Espèces de Gavials” (p. 59). Our Catalogues accordingly admit these groups of Crocodilia , under the generic names Alligator, Crocodilus, Gavialis . In the Section III, “Sur les Ossemens Fossiles de Crocodiles,” the vertebral, dental, and narial characters of the extinct species are defined, and those of the “Secondary” or “Mesozoic” formations are of higher value than he assigns to his recent “Subgenera;” but he forbears to invent special terms for