Evolutionary Patterns in Some Putative Australian Species in the Ant Genus Rhytidoponera

1986 ◽  
Vol 34 (4) ◽  
pp. 535 ◽  
Author(s):  
RH Crozier ◽  
P Pamilo ◽  
RW Taylor ◽  
YC Crozier
Keyword(s):  
Large Body ◽  
Correlation Coefficients ◽  
Principal Factor ◽  
Morphological Data ◽  
Data Sets ◽  
Large Species ◽  
Factor Scores ◽  
Allozyme Data ◽  
Data Set ◽  
Duplicate Locus

Genic and morphological variation were compared for 17 putative Rhytidoponera species and a species of the related genus Heteroponera, by use of an allozyme data set and one based on morphometric, surface sculpture, and pilosity characters. Each data set was considered in three versions: the raw data, principal factor scores normalized to the appropriate eigen vectors, and these scores range-coded. The agreement between these data sets, and similar sets derived from published vertebrate studies, was gauged by means of correlation coefficients between distance matrices based on them, calculated by a jack-knife procedure. In all cases, the raw allozyme data sets gave the highest correlation with the morphological sets, but none of the treatments of the morphological data was clearly superior in this regard to the others. For the ant data, congruence between the two types of data was also examined by comparing the branching orders of dendrograms (Wagner and REML), by a new test employing distributions based on the differences between randomly generated branching orders and a reference dendrogram. According to this test, the morphological dendrogram based on range-coded principal-factor scores was significantly more similar to that derived from the raw allozyme data than were those based on the other two treatments of the data. Differences in chromosome number do not correlate well with genic and morphological ones, which indicates that the speed of karyotype change in this genus has been highly variable. Some OTUS showed duplicate-locus expression for IDH, and clustering in the allozyme- based dendrograms occurred on the basis of IDH duplicate-locus expression pattern. The two 'victoriae' populations studied cluster closely with the metallica group on the morphology-based dendrograms, in agreement with conventional views that 'victoriae' is very close to 'metallica', but diverge markedly when allozymes are considered, which indicates that the morphological resemblance is probably due to convergence. The large genetic distance between these 'victoriae' populations indicates the likely presence of sibling species. R. 'tasrnaniensis' populations, in contrast, cluster strongly with 'metallica' in both morphology- and allozyme-based dendrograms. The marked divergence of scabra from other large species in the allozyme- based dendrograms indicates that its large body size has been derived independently.

Eucalypt phylogeny — molecules and morphology

1995 ◽  
Vol 8 (4) ◽  
pp. 483 ◽  
Author(s):  
PY Ladiges ◽  
F Udovicic ◽  
AN Drinnan
Keyword(s):  
Parallel Evolution ◽  
5S Rdna ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Morphological Data ◽  
Separate Analysis ◽  
Data Sets ◽  
Data Set ◽  
Seed Characters ◽  
Different Levels

Molecular (5S rDNA spacer and chloroplast DNA RnPs) and morphological data sets are informative at different levels of the eucalypt clade. They allow separate analysis of major subclades, the results of which, when combined, give a single, phylogenetic tree for Angophora Cav. and Eucalyptus L'Hér. For taxonomic revision, the tree supports the recognition of bloodwood eucalypts as monophyletic, but shows that informal subgenus Corymbia Pryor & Johnson is paraphyletic. The tree supports recognition of three major clades within the non-bloodwood eucalypts ('eudesmids', 'symphyomyrts' and 'monocalypts') and suggests relationships for taxa within each of these. Ovule and seed characters proved to be most informative in the morphological data set. The phylogenetic hypothesis suggests interpretations for homoplasious morphological characters, including parallel evolution of sepaline and petaline opercula (and associated stemonophore) and types of conflorescence.

scholarly journals Current Topics in Avian Conservation Genetics with Special Reference to the Southwestern Willow Flycatcher

2016 ◽  
Vol 9 (1) ◽  
pp. 60-69
Author(s):  
Robert M. Zink
Keyword(s):  
Analytical Methods ◽  
Scientific Method ◽  
Morphological Data ◽  
Data Sets ◽  
Avian Conservation ◽  
Full Data ◽  
Data Set ◽  
Willow Flycatcher ◽  
Existing Data ◽  
Conservation Decisions

It is sometimes said that scientists are entitled to their own opinions but not their own set of facts. This suggests that application of the scientific method ought to lead to a single conclusion from a given set of data. However, sometimes scientists have conflicting opinions about which analytical methods are most appropriate or which subsets of existing data are most relevant, resulting in different conclusions. Thus, scientists might actually lay claim to different sets of facts. However, if a contrary conclusion is reached by selecting a subset of data, this conclusion should be carefully scrutinized to determine whether consideration of the full data set leads to different conclusions. This is important because conservation agencies are required to consider all of the best available data and make a decision based on them. Therefore, exploring reasons why different conclusions are reached from the same body of data has relevance for management of species. The purpose of this paper was to explore how two groups of researchers can examine the same data and reach opposite conclusions in the case of the taxonomy of the endangered subspecies Southwestern Willow Flycatcher (Empidonax traillii extimus). It was shown that use of subsets of data and characters rather than reliance on entire data sets can explain conflicting conclusions. It was recommend that agencies tasked with making conservation decisions rely on analyses that include all relevant molecular, ecological, behavioral, and morphological data, which in this case show that the subspecies is not valid, and hence its listing is likely not warranted.

Considering Relationship of Proteins for Radiotherapy Prognosis of Bladder Cancer Cells in Small Data Set

2018 ◽  
Vol 57 (04) ◽  
pp. 220-229
Author(s):  
Tung-I Tsai ◽  
Yaofeng Zhang ◽  
Gy-Yi Chao ◽  
Cheng-Chieh Tsai ◽  
Zhigang Zhang
Keyword(s):  
Bladder Cancer ◽  
Expression Profiles ◽  
Correlation Coefficients ◽  
Value Theory ◽  
Training Data ◽  
Percentage Error ◽  
Small Data ◽  
Data Sets ◽  
Data Set ◽  
Protein Expression Profiles

Summary Background: Radiotherapy has serious side effects and thus requires prudent and cautious evaluation. However, obtaining protein expression profiles is expensive and timeconsuming, making it necessary to develop a theoretical and rational procedure for predicting the radiotherapy outcome for bladder cancer when working with limited data. Objective: A procedure for estimating the performance of radiotherapy is proposed in this research. The population domain (range of the population) of proteins and the relationships among proteins are considered to increase prediction accuracy. Methods: This research uses modified extreme value theory (MEVT), which is used to estimate the population domain of proteins, and correlation coefficients and prediction intervals to overcome the lack of knowledge regarding relationships among proteins. Results: When the size of the training data set was 5 samples, the mean absolute percentage error rate (MAPE) was 31.6200%; MAPE fell to 13.5505% when the number of samples was increased to 30. The standard deviation (SD) of forecasting error fell from 3.0609% for 5 samples to 1.2415% for 30 samples. These results show that the proposed procedure yields accurate and stable results, and is suitable for use with small data sets. Conclusions: The results show that considering the relationships among proteins is necessary when predicting the outcome of radiotherapy.

Phylogenetic analysis of the druid flies (Diptera: Schizophora: Clusiidae) based on morphological and molecular data

2010 ◽  
Vol 41 (3) ◽  
pp. 231-274 ◽  
Author(s):  
Jinzhong Fu ◽  
Owen Lonsdale ◽  
Brian Wiegmann ◽  
Stephen Marshall
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Cytochrome Oxidase Subunit ◽  
Data Set ◽  
Oxidase Subunit ◽  
Morphological And Molecular Data

AbstractIn this paper, the Clusiidae (Diptera: Schizophora) is analyzed phylogenetically using morphological and molecular data sets, and then redefined on the basis of derived morphological characters. The biology and distribution of the Clusiidae are also reviewed, a key is provided to the World genera, the status of the genus Craspedochaeta Czerny is reevaluated and the type of Heterochroa pictipennis Wulp is discussed. Molecular data sets include genomic DNA sequences from the mitochondrial genes COI (cytochrome oxidase subunit I) and COII (cytochrome oxidase subunit II), the large ribosomal nuclear subunit 28S, and the nuclear protein-coding carbomoylphosphate synthase (CPS) domain of CAD (or “rudimentary”). Genes were analyzed separately, in combination with each other, and in combination with a morphological data set. Although individual molecular data sets often provided conflicting phylogenetic signals, the topologies of the cladograms produced from each data set alone or in combination were largely similar. Most genus-level relationships and several basal divergences were unresolved, but Apiochaeta was very strongly and consistently supported as Sobarocephalinae, not Clusiinae. The Clusiinae and Sobarocephalinae are subsequently redefined using an adjusted morphological tree — retaining Apiochaeta in the Sobarocephalinae — that is only slightly longer (8.4%, or seven steps) than the most parsimonious tree. Our results illustrate the benefits of multiple independent data sets for phylogenetic reconstruction in order to verify and refine existing classifications.

Estimation of carcass composition by computer image analysis in the cross sections of cross-bred steers

1996 ◽  
Vol 76 (4) ◽  
pp. 497-506 ◽  
Author(s):  
A. B. Karnuah ◽  
K. Moriya ◽  
Y. Sasaki ◽  
K. Mitani ◽  
T. Yamazaki
Keyword(s):  
Image Analysis ◽  
Cross Section ◽  
Computer Image ◽  
Correlation Coefficients ◽  
Carcass Composition ◽  
Data Sets ◽  
Computer Image Analysis ◽  
Data Set ◽  
Stepwise Procedure ◽  
The Cross

Estimation equations for carcass composition were obtained using the information extracted from the carcass cross section by Computer Image Analysis (CIA). The total kilograms of lean, fat, and bone, and their percentages, were measured on the left side of the carcasses of F1 (cross-bred between Japanese Black and Holstein) steers by physical dissection. Traced data of the cross section between the 5th and 6th ribs (Data set I) and pictures of carcass cross section between the 7th and 8th ribs (Data set II) were subjected to image analysis. Various information on both the individual muscles and the overall outline of the cross section was extracted by the CIA technique. Maximum R2 improvement method of the stepwise procedure was used to choose the best regression equation to estimate carcass composition as total kilograms and percentages of lean, fat, and bone. The data sets were also adjusted for age and the stepwise procedure was also conducted. Coefficients of determination, adjusted for the degrees of freedom (adjusted R2) of the regression equations for estimating carcass composition, were high, i.e., 0.779 to 0.959 for kilograms of lean, fat, and bone, whereas for the percentages of lean, fat, and bone were high, i.e., 0.788 to 0.952, respectively. For the adjusted data, the adjusted R2 for estimating kilograms of lean, fat, and bone with Data sets I and II were 0.729, 0.633, and 0.598, and 0.813, 0.806, and 0.878, respectively, while for the percentages of lean, fat, and bone were 0.793, 0.623, and 0.378, and 0.953, 0.989, and 0.467, respectively. When the estimation equation obtained from the unadjusted Data set I was fitted with the information extracted from Data set II, the correlation coefficients between the values estimated by the equation and the values obtained by physical dissection on carcass composition were high, ranging from 0.70 to 0.92. On the other hand, the correlation coefficients obtained from the adjusted data sets were low. Key words: Estimation equation, computer image analysis, carcass composition, carcass cross section, F1 steers

Prediction of marsupial body mass

2001 ◽  
Vol 49 (2) ◽  
pp. 99 ◽  
Author(s):  
Troy J. Myers
Keyword(s):  
Body Mass ◽  
Correlation Coefficients ◽  
Data Sets ◽  
Error Statistics ◽  
Data Set ◽  
Fossil Species ◽  
Multiple Variable ◽  
Average Body Mass ◽  
Lower Molar ◽  
Average Body

Cranio-dental variables are correlated with body mass in marsupials, using a species data-set derived from extant australidelphian representatives, to predict body mass in fossil species. Thirty-eight extant australidelphian species, including 10 dasyuromorphians, 22 diprotodontians, 1 notoryctomorphian and 5 peramelemorphians, were analysed. Where sexual dimorphism was prominent, genders were evaluated separately. Twenty-nine cranio-dental variables were measured for each specimen and species averages calculated. Body masses were taken as recorded for each specimen or as published species averages. The cranio-dental measures for each morpho-species were then regressed against average body mass in four distinct data-sets: (1) the entire species sample, (2) only dasyuromorphian taxa, (3) only diprotodontians, and (4) all species excluding dasyuromorphians. Each cranio-dental variable was then ranked according to various error statistics and correlation coefficients. Results suggest that predictors of body size in eutherians (such as first lower molar area), commonly used to estimate body mass in marsupials may not be reliable or accurate indicators. Significant differences in the usefulness of predictor variables between taxonomic data-sets were also observed. Total jaw length is the most reliable predictor for diprotodontians, as well as for all species combined, whereas lower molar row length appears to be more appropriate for dasyuromorphians. Multiple variable regressions variably offer more precision than those derived from individual parameters. On the basis of these data, body mass estimations are provided for a number of extinct marsupial taxa.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

Detection and treatment of twinning: an improvement and new results

1999 ◽  
Vol 55 (6) ◽  
pp. 1179-1187 ◽  
Author(s):  
P. Dumas ◽  
E. Ennifar ◽  
P. Walter
Keyword(s):  
Correlation Coefficients ◽  
Initiation Site ◽  
Accurate Estimate ◽  
New Method ◽  
Data Sets ◽  
Additional Parameter ◽  
Data Set ◽  
Space Groups ◽  
Experimental Errors ◽  
Dimerization Initiation Site

This work deals with two aspects of the twinning problem. Firstly, an improvement of a known statistical test aimed at detecting twinning is presented and, secondly, a new parametrization of twinning is described, as well as a new method to obtain an accurate estimate of the degreee of twinning. During work on crystals of the dimerization-initiation site of the HIV-1 genomic RNA, perfectly twinned crystals were obtained which were not immediately recognized as such by use of a known statistical method. This method, reminiscent of Wilson tests for the detection of centrosymmetric space groups, relies on the calculation of 〈F^{2}〉/〈F〉2 or, equivalently, of 〈I 2〉/〈I〉2. It is shown that overlooking experimental errors may lead to erroneously large values of this index and, in turn, to ambiguous or incorrect conclusions. An immediate solution to this problem is presented. Independently, an alternative parametrization which expresses both the effect of twinning on intensities and the operation of untwinning to recover the correct intensities is proposed. A new method for estimating the degree of twinning is also presented. It is based upon maximization of the cross-correlation coefficients between intensities of all available data sets, and yields a fully analytical solution. Tests made with experimental data are quite satisfactory. It is suggested that the latter results could be used efficiently within the MIR method by allowing refinement, through one additional parameter only, of the twinning ratios of all data sets considered for phasing. Finally, the new parametrization of twinning has striking consequences in this correlation-based twinning determination: very unexpectedly, it yields a novel estimate of the `twinning ratio' of a potentially twinned crystal which is fully independent of the data set used for the comparison.

scholarly journals Controlling the correctness of retention parameters variations in reversed phase HPLC using recurrent relations

2021 ◽  
Vol 25 (2) ◽  
pp. 117-125
Author(s):  
Igor G. Zenkevich ◽  
◽  
Abdennour Derouiche ◽  
Darja A. Nikitina ◽  
Tatiana A. Kornilova ◽  
...  
Keyword(s):  
High Performance ◽  
Hydrate Formation ◽  
Correlation Coefficients ◽  
Reversed Phase ◽  
Data Sets ◽  
Data Set ◽  
Simple Method ◽  
Rp Hplc ◽  
Recurrent Relations ◽  
Retention Parameters

Recurrent approximation of analytes’ net retention times (tR) in reversed phase high performance liquid chromatography (RP HPLC) at different contents of organic constitu­ent in the eluent (C) is recommended as a method of revealing the reversible hydrate for­ma­tion. The criterion of that are the deviations of the dependences tR(С + DС) = atR(С) + b (*) from linearity, where DС is the constant increment of concentration variations; in our case DС = 5%. However, such deviations are rather small and, hence their measuring requires high robustness of the equipment involved. Besides hydrate formation, there are additional reasons for deviations, namely discrepancies between the real and the selected flows of the eluent. Compa­ring tR values obtained for the same analytes using the same chromatogra­phic column at the same conditions, but with different HPLC instruments using the systems methanol – water as the eluent confirms that tR values of one data set are equal only to approx. 76-98% tR values of another data set. Therefore, the eluent flow in the second case exceeds that in the first regime at the same pro­por­tion. The simple method for revealing such flow deviations is proposed. It is based on the recurrent approximation of tR = f(C) data sets for any compounds forming no hydrates in RP HPLC conditions (chlorobenzene was selected). The absence of the influ­en­ce of any distorted factors is confirmed with values of correlation coefficients for re­cur­rent depen­dencies (*) exceeding 0.999.

scholarly journals Reduced Sampling Frequency for Evaluating Fungicide Efficacy on Botrytis Fruit Rot of Strawberry

Plant Disease ◽  
2000 ◽  
Vol 84 (7) ◽  
pp. 743-748 ◽  
Author(s):  
D. E. Legard ◽  
F. G. Martin ◽  
C. L. Xiao ◽  
C. K. Chandler
Keyword(s):  
Production Systems ◽  
Rank Correlation ◽  
Correlation Coefficients ◽  
Complete Data ◽  
Fruit Rot ◽  
Data Sets ◽  
Marketable Yield ◽  
Data Set ◽  
Significant Difference ◽  
Fungicide Efficacy

Evaluating fungicide efficacy in annual strawberry production systems can be labor intensive due to continuous harvesting over a relatively long season. The effect of reduced harvest number on the accuracy of least significant difference (LSD) separations for Botrytis fruit rot (Botrytis cinerea) incidence and marketable yield in fungicide efficacy studies was evaluated over three seasons. Fruit were harvested and graded twice a week for a total of 23 to 32 harvests each season. Data from each season were divided into different sample sets. Data from three different harvest periods (early, late, and whole season) and different harvesting frequencies (twice weekly, once weekly, every second, third, or fourth week) were compared with the complete data set (twice weekly for the whole season). Spearman's rank correlation and Pearson's product moment correlation coefficients were used to evaluate the correlation of the complete data sets with data sets from other sampling plans. Harvesting once a week for either the late- or whole-season periods accurately estimated LSD groupings for Botrytis fruit rot incidence among fungicide treatments. The precision of marketable yield estimates using once-a-week harvesting for the late or whole-season periods were relatively lower than for the incidence of Botrytis.

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