Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix

Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates

10.7287/peerj.preprints.1596v1 ◽

2015 ◽

Cited By ~ 2

Author(s):

David Marjanović ◽

Michel Laurin

Keyword(s):

Phylogenetic Analysis ◽

Data Matrix ◽

Morphological Data ◽

Lower Jaw ◽

12 Steps ◽

The Matrix ◽

One Step ◽

The Difference ◽

Character Complexes ◽

The Many

The largest data matrix for phylogeny of early limbed vertebrates (Ruta M, Coates MI. 2007. J. Syst. Palaeont. 5:69–122) has supported controversial hypotheses; e.g., it has recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be one step more parsimonious than the “lepospondyl hypothesis” (LH). Scrutiny of the matrix reveals thousands of suboptimal scores (many clearly due to typographic and similar errors) as well as logically linked (redundant) characters, characters with only one described state, and even cases where taxa were scored after presumed relatives. Moreover, all characters – even obviously continuous ones – were unordered, effects of ontogeny were not sufficiently taken into account, and the authors mostly excluded data published after 2001, even their own. Our revised version – we document and justify all changes – yields much longer trees with a different topology, e.g. monophyletic Caudata, Diadectomorpha and (sometimes) Seymouriamorpha, Ichthyostega more rootward than Acanthostega, Anthracosauria more rootward than Temnospondyli, and the LH, which is 10 steps more parsimonious than the TH and 15 more than the “polyphyly hypothesis” (PH). Bootstrap values, though, are low, and few of the topologies are statistically distinguishable. For another set of analyses, we added 48 OTUs to the original 102. This destabilizes parts of the tree, e.g. the relationships of Anthracosauria and Temnospondyli. However, many of the added taxa have a fully resolved position or nearly so; this concerns the well-known Chroniosaurus (sister to a clade containing Solenodonsaurus, Seymouriamorpha, Diadectomorpha, Amniota and Amphibia), but also isolated lower-jaw material from the Devonian and Carboniferous. Despite the addition of Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton, the difference between LH and TH only shrinks to 9 steps, that between LH and PH to 13 steps. The “lepospondyl” Brachydectes is neither found as sister to Lissamphibia nor in the “microsaur” grade. Bootstrap values plummet, though, and all three hypotheses become statistically indistinguishable at p = 0.05. We then duplicated all analyses after coding all losses of bones as irreversible. Anthracosauria is then consistently placed more rootward than Temnospondyli; given the original taxon sample, the LH is 12 steps shorter than the “temnospondyl hypothesis” and 17 steps shorter than the PH, while the expanded taxon sample makes the LH 10 steps shorter than the TH and only 12 steps shorter than the PH. More robust results could likely be obtained by adding the many characters used in other analyses or discussed in the literature. We discuss phylogeny, approaches to coding, and certain character complexes, in particular the supposed middle ear of temnospondyls.

Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates

10.7287/peerj.preprints.1596v2 ◽

2016 ◽

Cited By ~ 1

Author(s):

David Marjanović ◽

Michel Laurin

Keyword(s):

Phylogenetic Analysis ◽

Data Matrix ◽

Morphological Data ◽

Published Data ◽

12 Steps ◽

The Matrix ◽

One Step ◽

The Difference ◽

Character Complexes ◽

The Impact

The largest published data matrix for phylogenetic analysis of Paleozoic limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) supported variously controversial hypotheses; e.g., it recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step. We report thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved – we document and justify all changes to the matrix –, but no characters are removed or added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega rootward of Acanthostega; Anthracosauria rootward of Temnospondyli which includes Caerorhachis; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained). We then added 48 OTUs to the original 102. This destabilizes some parts of the tree, e.g. the positions of Anthracosauria, Temnospondyli and Caerorhachis. Yet, many added taxa have well-resolved positions, ranging from the well known Chroniosaurus (Chroniosuchia), which lies just crownward of Temnospondyli and Gephyrostegidae, to isolated lower jaws. Even though Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 12 steps, that between LH and PH (R6) to 17 steps; the TH also requires several more regains of lost bones than the LH. Brachydectes (Lysorophia) is not found next to Lissamphibia. We duplicated all analyses after coding losses of bones as irreversible. The impact on the results is modest. Anthracosauria is always rootward of Temnospondyli. With 102 OTUs, the LH (R7) is 10 steps shorter than the TH (R8) and 11 steps shorter than the PH (R9); with 150, the LH (R10) is 14 steps shorter than the TH (R12) – and 13 steps shorter than the PH (R11). Bootstrap values are mostly low, and plummet when taxa are added. Statistically, the TH (R2, R5, R8, R12) is not distinguishable from the LH or the PH, but the LH (R1, R4, R7, 53 R10) and the PH (R3, R6, R9, R11) may be distinguishable from each other under both taxon samples and both reversibility settings. A reliable test is not available. We discuss the relationships of certain taxa, approaches to coding, some character complexes, and prospects for further improvement of this matrix.

Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates

10.7287/peerj.preprints.1596 ◽

2018 ◽

Author(s):

David Marjanović ◽

Michel Laurin

Keyword(s):

Phylogenetic Analysis ◽

Bayesian Inference ◽

Sister Group ◽

Data Matrix ◽

Morphological Data ◽

P Value ◽

The Matrix ◽

One Step ◽

The Difference ◽

Character Complexes

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered e.g. Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step. We report thousands of misscored cells, most of them due to typographic and similar accidental errors. Further, some characters are duplicated; some have only one described state; for some, most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved – we document and justify all changes to the matrix –, but no characters are added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; Anthracosauria either crownward or rootward of Temnospondyli; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, the sister-group of Lissamphibia is a large clade that includes adelogyrinids, urocordylid “nectrideans” and aïstopods. Adding 56 OTUs to the original 102 increases the resolution. The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Most bootstrap values are low, and plummet when taxa are added. Statistically, the TH (R2, R5) is not distinguishable from the LH or the PH; the LH (R1) and the PH (R3) may be distinguishable from each other under the original taxon sample at p ≥ 0.04. A test for the upper bound of the p value is not available. Bayesian inference (Analysis EB, same settings as R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and for the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes, and prospects for further improvement of this matrix. In its present state, even after our changes, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates; sufficient improvement, however, will be laborious but not difficult.

Reproducibility in phylogenetics: reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates

10.7287/peerj.preprints.1596v3 ◽

2018 ◽

Cited By ~ 1

Author(s):

David Marjanović ◽

Michel Laurin

Keyword(s):

Phylogenetic Analysis ◽

Bayesian Inference ◽

Sister Group ◽

Data Matrix ◽

Morphological Data ◽

P Value ◽

The Matrix ◽

One Step ◽

The Difference ◽

Character Complexes

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered e.g. Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step. We report thousands of misscored cells, most of them due to typographic and similar accidental errors. Further, some characters are duplicated; some have only one described state; for some, most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved – we document and justify all changes to the matrix –, but no characters are added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; Anthracosauria either crownward or rootward of Temnospondyli; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, the sister-group of Lissamphibia is a large clade that includes adelogyrinids, urocordylid “nectrideans” and aïstopods. Adding 56 OTUs to the original 102 increases the resolution. The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Most bootstrap values are low, and plummet when taxa are added. Statistically, the TH (R2, R5) is not distinguishable from the LH or the PH; the LH (R1) and the PH (R3) may be distinguishable from each other under the original taxon sample at p ≥ 0.04. A test for the upper bound of the p value is not available. Bayesian inference (Analysis EB, same settings as R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and for the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes, and prospects for further improvement of this matrix. In its present state, even after our changes, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates; sufficient improvement, however, will be laborious but not difficult.

Tem analysis of multiple-energy arsenic implanted and Rta'd silicon

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100126135 ◽

1987 ◽

Vol 45 ◽

pp. 246-247

Author(s):

R.A. Herring

Keyword(s):

Device Fabrication ◽

High Concentration ◽

Tem Analysis ◽

Defect Clusters ◽

High Fluences ◽

Small Defect ◽

Before And After ◽

The Matrix ◽

The Difference ◽

Factor Type

Rapid thermal annealing (RTA) of ion-implanted Si is important for device fabrication. The defect structures of 2.5, 4.0, and 6.0 MeV As-implanted silicon irradiated to fluences of 2E14, 4E14, and 6E14, respectively, have been analyzed by electron diffraction both before and after RTA at 1100°C for 10 seconds. At such high fluences and energies the implanted As ions change the Si from crystalline to amorphous. Three distinct amorphous regions emerge due to the three implantation energies used (Fig. 1). The amorphous regions are separated from each other by crystalline Si (marked L1, L2, and L3 in Fig. 1) which contains a high concentration of small defect clusters. The small defect clusters were similar to what had been determined earlier as being amorphous zones since their contrast was principally of the structure-factor type that arises due to the difference in extinction distance between the matrix and damage regions.

Development of Prolonged Delivery of Tramadol and Dissolution Translation by Statistical Data Treatment

International Journal of Pharmaceutical Sciences and Nanotechnology ◽

10.37285/ijpsn.2011.4.1.5 ◽

2011 ◽

Vol 4 (1) ◽

pp. 1331-1337

Author(s):

P B Parejiya ◽

B S Barot ◽

P K Shelat

Keyword(s):

Drug Release ◽

Study Data ◽

Stability Study ◽

Dissolution Time ◽

Matrix Tablet ◽

Burst Effect ◽

The Matrix ◽

The Mean ◽

The Difference ◽

Dissolution Efficiency

The present study was carried out to fabricate a prolonged design for tramadol using Kollidon SR (Polyvinyl acetate and povidone based matrix retarding polymer). Matrix tablet formulations were prepared by direct compression of Kollidon SR of a varying proportion with a fixed percentage of tramadol. Tablets containing a 1:0.5 (Drug: Kollidon SR) ratio exhibited a rapid rate of drug release with an initial burst effect. Incorporation of more Kollidon SR in the matrix tablet extended the release of drug with subsequent minimization of the burst effect as confirmed by the mean dissolution time, dissolution efficiency and f2 value. Among the formulation batches, a direct relationship was obtained between release rate and the percentage of Kollidon SR used. The formulation showed close resemblance to the commercial product Contramal and compliance with USP specification. The results were explored and explained by the difference of micromeritic characteristics of the polymers and blend of drug with excipients. Insignificant effects of various factors, e.g. pH of dissolution media, ionic strength, speed of paddle were found on the drug release from Kollidon-SR matrix. The formulation followed the Higuchi kinetic model of drug release. Stability study data indicated stable character of Batch T6 after short-term stability study.

ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects

Bioinformatics ◽

10.1093/bioinformatics/btab179 ◽

2021 ◽

Author(s):

Irzam Sarfraz ◽

Muhammad Asif ◽

Joshua D Campbell

Keyword(s):

Single Cell ◽

R Package ◽

Poor Quality ◽

Data Matrix ◽

Supplementary Information ◽

Data Provenance ◽

Rna Seq ◽

Efficient Management ◽

The Matrix ◽

The Relationship

Abstract Motivation R Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for storing one or more matrix-like assays along with associated row and column data. These objects have been used to facilitate the storage and analysis of high-throughput genomic data generated from technologies such as single-cell RNA sequencing. One common computational task in many genomics analysis workflows is to perform subsetting of the data matrix before applying down-stream analytical methods. For example, one may need to subset the columns of the assay matrix to exclude poor-quality samples or subset the rows of the matrix to select the most variable features. Traditionally, a second object is created that contains the desired subset of assay from the original object. However, this approach is inefficient as it requires the creation of an additional object containing a copy of the original assay and leads to challenges with data provenance. Results To overcome these challenges, we developed an R package called ExperimentSubset, which is a data container that implements classes for efficient storage and streamlined retrieval of assays that have been subsetted by rows and/or columns. These classes are able to inherently provide data provenance by maintaining the relationship between the subsetted and parent assays. We demonstrate the utility of this package on a single-cell RNA-seq dataset by storing and retrieving subsets at different stages of the analysis while maintaining a lower memory footprint. Overall, the ExperimentSubset is a flexible container for the efficient management of subsets. Availability and implementation ExperimentSubset package is available at Bioconductor: https://bioconductor.org/packages/ExperimentSubset/ and Github: https://github.com/campbio/ExperimentSubset. Supplementary information Supplementary data are available at Bioinformatics online.

Impact of AMSU-A Radiances in a Column Ensemble Kalman Filter

Monthly Weather Review ◽

10.1175/mwr-d-18-0093.1 ◽

2018 ◽

Vol 146 (12) ◽

pp. 3949-3976 ◽

Cited By ~ 2

Author(s):

Herschel L. Mitchell ◽

P. L. Houtekamer ◽

Sylvain Heilliette

Keyword(s):

Covariance Matrix ◽

Background Error ◽

Error Covariance Matrix ◽

Background Error Covariance ◽

Error Covariance ◽

Microwave Sounding Unit ◽

The Matrix ◽

Microwave Sounding ◽

Background Temperature ◽

The Difference

Abstract A column EnKF, based on the Canadian global EnKF and using the RTTOV radiative transfer (RT) model, is employed to investigate issues relating to the EnKF assimilation of Advanced Microwave Sounding Unit-A (AMSU-A) radiance measurements. Experiments are performed with large and small ensembles, with and without localization. Three different descriptions of background temperature error are considered: 1) using analytical vertical modes and hypothetical spectra, 2) using the vertical modes and spectrum of a covariance matrix obtained from the global EnKF after 2 weeks of cycling, and 3) using the vertical modes and spectrum of the static background error covariance matrix employed to initiate a global data assimilation cycle. It is found that the EnKF performs well in some of the experiments with background error description 1, and yields modest error reductions with background error description 3. However, the EnKF is virtually unable to reduce the background error (even when using a large ensemble) with background error description 2. To analyze these results, the different background error descriptions are viewed through the prism of the RT model by comparing the trace of the matrix , where is the RT model and is the background error covariance matrix. Indeed, this comparison is found to explain the difference in the results obtained, which relates to the degree to which deep modes are, or are not, present in the different background error covariances. The results suggest that, after 2 weeks of cycling, the global EnKF has virtually eliminated all background error structures that can be “seen” by the AMSU-A radiances.

V.—Mr. Harkee and Mr. Debley on the Scandinavian Ice-Sheet

Geological Magazine ◽

10.1017/s0016756800143936 ◽

1894 ◽

Vol 1 (11) ◽

pp. 496-499

Author(s):

Henry H. Howorth

Keyword(s):

Ice Sheet ◽

Good Effect ◽

The North ◽

The Matrix ◽

Glacier Ice ◽

Inductive Methods ◽

The North Sea ◽

Antarctic Continent ◽

The Alps ◽

The Difference

Mr. Deeley tells your readers that he has recently been to the summit of Mont Blanc, and has been studying the difference between névé and glacier ice. This is interesting; but we thought that a great many people had done the same thing during the last hundred years, and we thought that one of them, Forbes, had studied the famous Mountain and the phenomenoninquestion to good effect, not in a casual visit to the Alps, but in the course of many years of patient labour. Among other things we also thought he had shown that in a viscous body like ice, the slope of the upper surface necessary to make it begin to move is the same as the slope which, would be required to induce motion in the ice if its bed were inclined at an angle. He further collected considerable evidence to show what the least angle is upon which ice will begin to move. This is the slope, the least slope, available. It is nothing less than astounding to me that anyone should venture to postulate a Scand in avian ice-sheet in the North Sea until he had considered this necessary factor, and how it would operate.The Scand in avian ice-sheet was, I believe, the invention of Croll, who, sittinginhis arm-chair and endowed with a brilliant imagination, imposed upon sober science this extraordinary postulate. He did not dream of testing it by an examination of the coasts of Norway, or even of Britain, but put it forward apparently as a magnificent deduction. All deductions untested by experiment are dangerous. Thus it came about that the great monster which is said to have come from Norway, goodness knows by what mechanical process, speedily dissolved away on the application of inductive methods. Of course it still maintained its hold upon that section, of geologists who dogmatiseinprint a great deal about the Glacial period before they have ever seen a glacier at work at all; but I am speaking of those who have studied the problem inductively. First Mr. James Geikie, a disciple of Croll, was obliged to confess that this ice-sheet, which is actually said to have advanced as far as the hundred-fathom line in the Atlantic, and there presented a cliff of ice like the Antarctic continent, never can have reached the Faroes, which had an ice-sheet of their own. Next Messrs. Peach and Home were constrained to admit that no traces of it of any kind occur in the Orkneys, or in Eastern Scotland. They still maintained its presence in the Shetlands; however, this was upon evidence which is somewhat extraordinary. I do not mean the evidence as to the direction of the striation, which was so roughly handled by Mr. Milne-Home, but I mean the evidence they adduce that the boulders found on the islands are apparently all local ones, and that, contrary to the deposits of glaciers, they diminish in number as we recede from the matrix whence they were derived.

PENERAPAN METODE MULTI ATTRIBUTE UTILITY THEORY (MAUT) DALAM PEMETAAN TINGKAT DAMPAK BENCANA BANJIR DI KABUPATEN BANTUL

Telematika ◽

10.31315/telematika.v17i1.3402 ◽

2020 ◽

Vol 17 (1) ◽

pp. 26

Author(s):

Afif Irfan Abdurrahman ◽

Bambang Yuwono ◽

Yuli Fauziah

Keyword(s):

Utility Theory ◽

Matrix Multiplication ◽

Flood Disaster ◽

Accuracy Rate ◽

Affected Area ◽

A Value ◽

Multi Attribute Utility Theory ◽

The Matrix ◽

The Difference ◽

The Impact

Flood disaster is a dangerous disaster, an event that occurs due to overflow of water resulting in submerged land is called a flood disaster. Almost every year Bantul Regency is affected by floods due to high rainfall. The flood disaster that struck in Bantul Regency made the Bantul District Disaster Management Agency (BPBD) difficult to handle so that it needed a mapping of the level of the impact of the flood disaster to minimize the occurrence of floods and provide information to the public.This study will create a system to map the level of impact of floods in Bantul Regency with a decision support method namely Multi Attribute Utility Theory (MAUT). The MAUT method stage in determining the level of impact of flood disasters through the process of normalization and matrix multiplication. The method helps in determining the areas affected by floods, by managing the Indonesian Disaster Information Data (DIBI). The data managed is data on criteria for the death toll, lost victims, damage to houses, damage to public facilities, and damage to roads. Each criteria data has a value that can be used to determine the level of impact of a flood disaster. The stages for determining the level of impact of a disaster require a weighting calculation process. The results of the weighting process display the scoring value which has a value of 1 = low, 2 = moderate, 3 = high. To assist in determining the affected areas using the matrix normalization and multiplication process the process is the application of the Multi Attribute Utility Theory (MAUT) method.This study resulted in a mapping of the level of impact displayed on google maps. The map view shows the affected area points and the level of impact of the flood disaster in Bantul Regency. The mapping produced from the DIBI data in 2017 produced the highest affected area in the Imogiri sub-district. The results of testing the data can be concluded that the results of this study have an accuracy rate of 95% when compared with the results of the mapping previously carried out by BPBD Bantul Regency. The difference in the level of accuracy is because the criteria data used are not the same as the criteria data used by BPBD in Bantul Regency so that the accuracy rate is 95%.