scholarly journals Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

2021 ◽  
Author(s):  
Tina Begum ◽  
Martha Liliana Serrano‐Serrano ◽  
Marc Robinson‐Rechavi
Keyword(s):  
Pairwise Comparison ◽  
Trait Evolution ◽  
Contrast Method ◽  
Independent Contrast

scholarly journals Correlated evolution and independent contrasts

1997 ◽  
Vol 352 (1352) ◽  
pp. 519-529 ◽  
Author(s):  
Trevor Price
Keyword(s):  
Adaptive Radiation ◽  
Related Species ◽  
Past History ◽  
Evolutionary Model ◽  
Closely Related Species ◽  
Correlated Evolution ◽  
Mean Values ◽  
Contrast Method ◽  
Independent Contrast

The use of the independent contrast method in comparative tests is studied. It is assumed that: (i) the traits under investigation are subject to natural selection; (ii) closely related species are similar because they share many characteristics of their niche, inherited from a common ancestor; and (iii) the current adaptive significance of the traits is the focus of investigation. The main objection to the use of species values in this case is that third variables which are shared by closely related species confound the relationship between the focal traits. In this paper, I argue that third variables are largely not controlled by the contrast methods, which are designed to estimate correlated evolution. To the extent that third variables also show correlated evolution, the true relationship among the traits of interest will remain obscured. Although the independent contrast method does not resolve the influence of third traits it does, in principle, provide a greater resolution than the use of the species mean values. However, its validity depends on the applicability of an evolutionary model which has a substantial stochastic component. To illustrate the consequences of relaxing this assumption I consider an alternative model on an adaptive radiation, where species come to fill a fixed niche space. Under this model, the expected value for the contrast correlation differs from that for the species correlation. The two correlations differ because contrasts reflect the historical pattern of diversification among species, whereas the species values describe the present–day relationships among the species. If the latter is of interest, I suggest that assessing significance based on the species correlations can be justified, providing that attention is paid to the role of potentially confounding third traits. Often, differences between contrast and species correlations may be biologically informative, reflecting changes in correlations between traits as an adaptive radiation proceeds; contrasts may be particularly useful as a means of investigating past history, rather than current utility of traits.

scholarly journals Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

2020 ◽  
Author(s):  
Tina Begum ◽  
Martha Liliana Serrano-Serrano ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Function ◽  
Evolutionary Biology ◽  
Pairwise Comparison ◽  
Simulation Models ◽  
Functional Trait ◽  
Gene Family Evolution ◽  
Pairwise Comparisons ◽  
Independent Contrasts ◽  
Functional Evolution ◽  
Trait Evolution

AbstractDespite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystalized methodological questions is the “ortholog conjecture”, the hypothesis that function evolves faster after duplication (i.e., in paralogs), and conversely conserved between orthologs. Since the mode of functional evolution after duplication is not well known, we investigate under what reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologs and paralogs.We investigate three different simulation models, which represent reasonable but simplified hypotheses about gene function (our “trait”) evolution. These are time dependent trait acceleration, correlated changes in rates of both sequence and trait evolution, and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age.Both approaches loose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the ortholog conjecture under ortholog conjecture simulations by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well to trace rapid shift in traits.Considering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution.

scholarly journals A Phylogenetic Independent Contrast Method under the Ornstein-Uhlenbeck Model and its Applications in Correlated Evolution

2021 ◽  
Author(s):  
Cong Liang ◽  
Yingjun Deng
Keyword(s):  
Least Squares ◽  
Generalized Least Squares ◽  
Comparative Methods ◽  
Stabilizing Selection ◽  
Type I ◽  
Phylogenetic Comparative Methods ◽  
Trait Evolution ◽  
Correlated Evolution ◽  
Independent Contrast ◽  
Pic Method

Phylogenetic comparative methods are essential in studying the evolution of traits across a phylogeny. Felsenstein's phylogenetic independent contrast (PIC) method and the generalized least squares (GLS) regression were often utilized to study whether evolutionary changes between traits were correlated. However, a neutral Brownian model is assumed in the PIC method, which impacts the performance of the PIC method when the trait is subject to adaptation. In recent years, the Ornstein-Uhlenbeck (OU) model has attracted increasing attention in studying the evolution of traits with stabilizing selection. In this study, we extended Felsenstein's PIC method under the OU model, which we termed OU-PIC. We simulated trait evolution under the OU model on phylogenetic trees with 8, 10, and 55 species. Compared to the PIC method, the OU-PIC method with correct stabilizing selection parameters achieved an appropriate type I error rate, the highest test power, and the lowest mean squared error. We presented a concise proof of the intrinsic connection between the OU-PIC and the generalized least squares (GLS) regression method in evaluating correlated evolution under the OU model. The OU-PIC method has a broad range of applications when trait evolution could be sufficiently modeled by the OU process. Compared with other phylogenetic comparative methods, OU-PIC avoids the inverse of the covariance matrix and would facilitate the analysis of correlated evolution on large phylogenies.

Video-Enhanced Microscopy--Better Visibility of Plant Cell Structures

1982 ◽  
Vol 40 ◽  
pp. 182-185
Author(s):  
N.S. Allen ◽  
R.D. Allen
Keyword(s):  
Diffraction Pattern ◽  
Theoretical Basis ◽  
Numerical Aperture ◽  
Gain Control ◽  
Control Unit ◽  
Camera Control ◽  
Variable Gain ◽  
Contrast Method ◽  
Fine Detail ◽  
Cell Structures

Various methods of video-enhanced microscopy combine TV cameras with light microscopes creating images with improved resolution, contrast and visibility of fine detail, which can be recorded rapidly and relatively inexpensively. The AVEC (Allen Video-enhanced Contrast) method avoids polarizing rectifiers, since the microscope is operated at retardations of λ/9- λ/4, where no anomaly is seen in the Airy diffraction pattern. The iris diaphram is opened fully to match the numerical aperture of the condenser to that of the objective. Under these conditions, no image can be realized either by eye or photographically. Yet the image becomes visible using the Hamamatsu C-1000-01 binary camera, if the camera control unit is equipped with variable gain control and an offset knob (which sets a clamp voltage of a D.C. restoration circuit). The theoretical basis for these improvements has been described.

Penilaian Kinerja Dosen Dengan Menggunakan Metode AHP Studi Kasus di STIE Ahmad Dahlan Jakarta

Liquidity ◽  
2018 ◽  
Vol 2 (1) ◽  
pp. 100-109
Author(s):  
Ellya Sestri
Keyword(s):  
Decision Making ◽  
Performance Appraisal ◽  
Technological Progress ◽  
Pairwise Comparison ◽  
Relative Importance ◽  
Faculty Performance ◽  
Business World ◽  
The Face ◽  
Hierarchy Process ◽  
Rule Out

An increasingly rapid technological progress in the era of globalization in the business world, so do not rule out the possibility that a decision-making is something that is very vital in determining the decisions to be taken in the face of competitive business world. Decision making can be influenced by several aspects, this can affect the speed of decision making by the decision maker in which decisions must be quick and accurate. Lecturer Performance Assessment Using the Analytical Hierarchy Process is a decision support system that aims to assess faculty performance according to certain criteria. This system of faculty performance appraisal criteria to map a hierarchy, where each hierarchy will be performed pairwise comparison, the pairwise comparisons between criteria, so to get a comparison of the relative importance of criteria with each other. The results of this comparison is then analyzed to obtain the priority of each criterion. Once completed and performed an assessment of alternative options to be compared and calculated to obtain the best alternatives according to established criteria.

DETERMINING THE DESALINATION UNIT COMPOSITION FOR COSTAL AREAS AND SMALL ISLANDS USE ANALYTIC HIERARCHY PROCESS

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Imam Setiadi ◽  
Dinda Rita K. Hartaja
Keyword(s):  
Analytic Hierarchy Process ◽  
Energy Demand ◽  
Pairwise Comparison ◽  
Small Islands ◽  
Ahp Method ◽  
Analytic Hierarchy ◽  
Comparison Research ◽  
Hierarchy Process ◽  
Selection Of

Selection of the appropriate composition desalination units can be done with a variety of method approaches, one of the method is the Analytic Hierarchy Process. In determining the desalination unit with AHP method to consider is setting a goal, an alternative criteria and pairwise comparison. Research for the determination of the exact composition of the desalination unit in order to achieve sustainable drinking water suppy in coastal areas and small islands has been conducted. The results of the study are as follows, the energy demand of 50.83%, operator costs of 26.64%, maintenance costs of 14.13% and chemical requirement 8.4%. For an alternative composition desalination unit of RO 10 m3 / day is the best alternative composition with value of 59.61%, the composition of the next alternative is RO 20 m3/ day of 30.40% and the last alternative of the desalination unit composition is RO 120 m3/ day of 09.99%.Key words : Desalination, Mukti Stage Flash Composition, AHP

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