scholarly journals Characterizing and comparing phylogenies from their Laplacian spectrum

2015 ◽  
Author(s):  
Eric Lewitus ◽  
Helene Morlon
Keyword(s):  
Population Genetics ◽  
Spectral Density ◽  
Phylogenetic Trees ◽  
Life Sciences ◽  
Laplacian Spectrum ◽  
Density Profiles ◽  
Spectral Graph ◽  
Research Areas ◽  
Graph Theoretical Approach ◽  
Comprehensive Framework

Phylogenetic trees are central to many areas of biology, ranging from population genetics and epidemiology to microbiology, ecology, and macroevolution. The ability to summarize properties of trees, compare different trees, and identify distinct modes of division within trees is essential to all these research areas. But despite wide-ranging applications, there currently exists no common, comprehensive framework for such analyses. Here we present a graph-theoretical approach that provides such a framework. We show how to construct the spectral density profiles of phylogenetic trees from their Laplacian graphs. Using ultrametric simulated trees as well as non-ultrametric empirical trees, we demonstrate that the spectral density successfully identifies various properties of the trees and clusters them into meaningful groups. Finally, we illustrate how the eigengap can identify modes of division within a given tree. As phylogenetic data continue to accumulate and to be integrated into various areas of the life sciences, we expect that this spectral graph-theoretical framework to phylogenetics will have powerful and long-lasting applications.

Evolution, genetics, and systematics

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Population Genetics ◽  
Sexual Selection ◽  
Fossil Record ◽  
Life Sciences ◽  
Altruistic Behavior ◽  
Synthetic Theory ◽  
Theory Of Evolution ◽  
Evolution By Natural Selection ◽  
Current Paradigm ◽  
Epigenetic Processes

This chapter starts with the general principles of the theory of evolution by natural selection advanced by Darwin and the Mendelian theory of heredity. Next comes consideration of the “new-Darwinian synthesis” or “synthetic theory,” which integrates both precedents into what has become the current paradigm of the life sciences. Molecular evolution and population genetics follow, including epigenetic processes. Next, special models of selection are considered, such as sexual selection and the models that account for altruistic behavior. After the mechanisms of speciation, the main concepts of systematics are explored, which facilitate understanding of different traits. The chapter finally explores the fundamental concepts of taxonomy and the methods from phenetics to cladistics, that makes it possible to evaluate the diversity of organisms and the methods for dating the fossil record.

scholarly journals Extremal Values of the Sackin Tree Balance Index

2021 ◽  
Author(s):  
Mareike Fischer
Keyword(s):  
Phylogenetic Trees ◽  
Theoretical Computer Science ◽  
Search Trees ◽  
Formal Proofs ◽  
Birth Process ◽  
Ordered Trees ◽  
Research Areas ◽  
New Findings ◽  
Mathematical Phylogenetics ◽  
Extremal Values

AbstractTree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are more likely than balanced ones. Also, concerning ordered search trees, more balanced ones allow for more efficient data structuring than imbalanced ones. Therefore, different methods to measure the balance of trees were introduced. The Sackin index is one of the most frequently used measures for this purpose. In many contexts, statements about the minimal and maximal values of this index have been discussed, but formal proofs have only been provided for some of them, and only in the context of ordered binary (search) trees, not for general rooted trees. Moreover, while the number of trees with maximal Sackin index as well as the number of trees with minimal Sackin index when the number of leaves is a power of 2 are relatively easy to understand, the number of trees with minimal Sackin index for all other numbers of leaves has been completely unknown. In this manuscript, we extend the findings on trees with minimal and maximal Sackin indices from the literature on ordered trees and subsequently use our results to provide formulas to explicitly calculate the numbers of such trees. We also extend previous studies by analyzing the case when the underlying trees need not be binary. Finally, we use our results to contribute both to the phylogenetic as well as the computer scientific literature using the new findings on Sackin minimal and maximal trees to derive formulas to calculate the number of both minimal and maximal phylogenetic trees as well as minimal and maximal ordered trees both in the binary and non-binary settings. All our results have been implemented in the Mathematica package SackinMinimizer, which has been made publicly available.

A Spectral Graph Theoretical Approach to Oriented Energy Features

2017 ◽  
Vol 31 (01) ◽  
pp. 1755001 ◽  
Author(s):  
Güleser Kalaycı Demir
Keyword(s):  
Theoretical Approach ◽  
Graph Laplacian ◽  
Texture Segmentation ◽  
Contour Detection ◽  
Feature Extraction Method ◽  
Spectral Graph ◽  
Graph Theoretical Approach ◽  
Novel Method ◽  
Oriented Energy ◽  
Complex Valued

In this work, we propose a novel method for determining oriented energy features of an image. Oriented energy features, useful for many machine vision applications like contour detection, texture segmentation and motion analysis, are determined from the filters whose outputs are enhanced at the edges of the image at a given orientation. We use the eigenvectors and eigenvalues of graph Laplacian for determining the oriented energy features of an image. Our method is based on spectral graph theoretical approach in which a graph is assigned complex-valued edge weights whose phases encode orientation information. These edge weights give rise to a complex-valued Hermitian Laplacian whose spectrum enables us to extract oriented energy features of the image. We perform a set of numerical experiments to determine the efficiency and characteristics of the proposed method. In addition, we apply our feature extraction method to texture segmentation problem. We do this in comparison with other known methods, and show that our method performs better for various test textures.

scholarly journals Genealogical inference of closely related species based on microsatellites

2001 ◽  
Vol 78 (3) ◽  
pp. 209-212 ◽  
Author(s):  
CHRISTIAN SCHLÖTTERER
Keyword(s):  
Population Genetics ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Microsatellite Analysis ◽  
Closely Related Species ◽  
Research Areas

Despite their unmatched popularity in many research areas, microsatellites have not yet become a major tool for the inference of genealogical relationships of closely related species. Recent studies have successfully extended the repertoire of microsatellite analysis beyond population genetics and demonstrate that phylogenetic relationships of closely related species can be inferred accurately with fewer loci than previously assumed.

scholarly journals Scientometric analysis activity in the publication «life sciences» in the world and in Ukraine

2019 ◽  
pp. 23-33
Author(s):  
V.M. Yevtushenko
Keyword(s):  
Core Collection ◽  
Web Of Science ◽  
Journal Citation Report ◽  
Life Sciences ◽  
Scientometric Analysis ◽  
Research Areas ◽  
The World ◽  
Scientific Papers ◽  
Scientific Fields ◽  
The Web

The article is devoted to the study of the state and trends of the publishing activity of Ukrainian scientists and leading countries in the field of life sciences («Life sciences»). The Web of Science Core Collection (WoS CC), Journal Citation Report (JSR) and InCites, as well as classifications of scientific fields designed to structure the publication flow of scientific papers and journals in these information resources, are used for the research base – Web of Science Categories and Research Areas. The article presents the results of the author’s research on the publication indices of scientists of Ukraine and the leading countries of the world for the period 2008-2018 in the field of “Life Sciences” according to the international science-computer database of Web of Science. Conclusions about the growth of indicators of publication activity of scientific works in the field of “Life Sciences” are made. The tendency of a significant increase in their number in Ukraine has been revealed, but domestic studies do not represent all the areas of «Life Sciences» most popular in foreign scientists

Evolution: medicine’s most basic science

2010 ◽  
pp. 12-15 ◽  
Author(s):  
Randolph M. Nesse ◽  
Richard Dawkins
Keyword(s):  
Population Genetics ◽  
Basic Science ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Evolutionary Methods

The role of evolutionary biology as a basic science for medicine has been expanding rapidly. Some evolutionary methods are already widely applied in medicine, such as population genetics and methods for analysing phylogenetic trees. Newer applications come from seeking evolutionary as well as proximate explanations for disease. ...

Evolution: Medicine’s most basic science

2020 ◽  
pp. 39-42
Author(s):  
Randolph M. Nesse ◽  
Richard Dawkins
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Basic Science ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
The Body ◽  
Clinical Implications ◽  
Trade Offs ◽  
The Cost

The role of evolutionary biology as a basic science for medicine is expanding rapidly. Some evolutionary methods are already widely applied in medicine, such as population genetics and methods for analysing phylogenetic trees. Newer applications come from seeking evolutionary as well as proximate explanations for disease. Traditional medical research is restricted to proximate studies of the body’s mechanism, but separate evolutionary explanations are needed for why natural selection has left many aspects of the body vulnerable to disease. There are six main possibilities: mismatch, infection, constraints, trade-offs, reproduction at the cost of health, and adaptive defences. Like other basic sciences, evolutionary biology has limited direct clinical implications, but it provides essential research methods, encourages asking new questions that foster a deeper understanding of disease, and provides a framework that organizes the facts of medicine.

scholarly journals Further Effects of Phylogenetic Tree Style on Student Comprehension in an Introductory Biology Course

2018 ◽  
Vol 17 (2) ◽  
pp. ar17 ◽  
Author(s):  
Jonathan Dees ◽  
Caitlin Bussard ◽  
Jennifer L. Momsen
Keyword(s):  
Phylogenetic Trees ◽  
Life Sciences ◽  
Biology Education ◽  
Student Understanding ◽  
Introductory Biology ◽  
Student Comprehension ◽  
Construction Tasks ◽  
Based Instruction ◽  
Introductory Biology Course ◽  
The Impact

Phylogenetic trees have become increasingly important across the life sciences, and as a result, learning to interpret and reason from these diagrams is now an essential component of biology education. Unfortunately, students often struggle to understand phylogenetic trees. Style (i.e., diagonal or bracket) is one factor that has been observed to impact how students interpret phylogenetic trees, and one goal of this research was to investigate these style effects across an introductory biology course. In addition, we investigated the impact of instruction that integrated diagonal and bracket phylogenetic trees equally. Before instruction, students were significantly more accurate with the bracket style for a variety of interpretation and construction tasks. After instruction, however, students were significantly more accurate only for construction tasks and interpretations involving taxa relatedness when using the bracket style. Thus, instruction that used both styles equally mitigated some, but not all, style effects. These results inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

Summary of Final Report: Space life sciences planning workshop (SLSPW) June 5-7, 2000 Mont Tremblant, Québec

2001 ◽  
Vol 79 (9) ◽  
pp. 741-743 ◽  
Author(s):  
John R Ledsome
Keyword(s):  
Bone Loss ◽  
Life Sciences ◽  
Final Report ◽  
Muscle Loss ◽  
Major Research ◽  
Future Directions ◽  
Research Areas ◽  
Space Agency ◽  
The Future ◽  
Key Questions

A Space Life Sciences Planning Workshop was sponsored by the Canadian Space Agency to identify key questions in the major research areas supported by the Life Sciences Program, to identify Canadian strengths and capabilities as they relate to these research areas, and to make recommendations for the future directions of the Life Sciences Program. The conclusions reached by the workshop participants have been presented to the Canadian Space Agency. This report is a summary of those conclusions.Key words: microgravity, Canadian Space Agency, bone loss, muscle loss, cardiovascular, radiation, neuroscience.

scholarly journals On the Adjacency, Laplacian, and Signless Laplacian Spectrum of Coalescence of Complete Graphs

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
S. R. Jog ◽  
Raju Kotambari
Keyword(s):  
Line Graph ◽  
Laplacian Matrix ◽  
Spectral Graph Theory ◽  
Complete Graphs ◽  
Laplacian Spectrum ◽  
Spectral Graph ◽  
Signless Laplacian Spectrum ◽  
Subdivision Graph ◽  
Laplacian Energy ◽  
Signless Laplacian

Coalescence as one of the operations on a pair of graphs is significant due to its simple form of chromatic polynomial. The adjacency matrix, Laplacian matrix, and signless Laplacian matrix are common matrices usually considered for discussion under spectral graph theory. In this paper, we compute adjacency, Laplacian, and signless Laplacian energy (Qenergy) of coalescence of pair of complete graphs. Also, as an application, we obtain the adjacency energy of subdivision graph and line graph of coalescence from itsQenergy.

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