To browse Academia. Skip to main content. Log In Sign Up. Molecular Evolution A Phylogenetic Approach. Jonathan Miller. P34 eb ddc: Page University of Glasgow Edward C. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Actwithout the prior permission of the copyright owner.
Page, Edward C. Includes bibliographical references and index. ISBN 1. Molecular evolution. Evolutionary genetics.
Holmes, Edward C. P34 This, of course, was merely a fortuitous coincidence. In any event, Antje's gentle prodding helped speed the completion of one half of the book. Ian Sherman shepherded the book to its conclusion with great patience in the face of our ludicrously optimistic assessments of when we would be finished. Jake Baum's input into part of Chapter 4 was also much appreciated. But this is exactly what happened in July when the entire DNA base pairs of its genome was publishedthe first of a free-living organism.
A new era in biological science had begun. Soon after Haemophilus influenzae came the first complete genome from a eukaryotethat of the yeast Saccharomyces cerevisiae, followed by Methanococcus jannaschii, the first representative of the third domain of cellular life, the Archaea. In the next few years molecular biology will claim its biggest prizethe 3. DNA sequences are valuable because they provide the most detailed anatomy possible for any organismthe instructions for how each working part should be assembled and operate.
Much of modern biology now relies on unravelling the information stored within gene sequences and this is true of evolutionary studies, where gene sequences are now recognised as an invaluable document of the history of life on earth. It is the aim of this book to show what evolutionary information is written into gene sequences and how this information might be recovered. This is the science of molecular evolution. Take, for example, Haemophilus influenzae, Saccharomyces cerevisiae and Methanococcus jannaschii.The strength of the activity is its depth and interdisciplinary approach.
This activity reinforces the interdisciplinary nature of modern science. Students utilize real data from real scientists. Students apply the principles of evolution in their reasoning to make use of this data from geology and biological science. For purposes of this publication, I have placed the student activity in the beginning followed by teacher information and my discussion of possible solutions.
By their very nature, islands are isolated and are essentially a living laboratory of evolution. In this investigation, you should be familiar with the terms speciation, geographic isolation, gene flow, gene pool, and reproductive isolation. You will work with real data from real populations. The data will include observations of lizard morphology body formgeological age estimates of various islands in the Canary Island Archipelago, geographic distances, and genetic distances based on nucleotide base differences in DNA between different populations of lizards.
The Canary Islands form an archipelago of seven volcanic islands just west of the African continent Map 1. The island chain starts about 85 km 50 miles west of the continent, following a fault line of the Atlas Mountains in northern Africa. Geologists theorize that a geologic hot spot of upwelling magma has been drifting westward for the past 20 million years, gradually forming the islands as it moves.
Thus the most eastern island, Lanzarote, is oldest, while the smaller western island, Hierro, is the youngest, about 0. Volcanic islands are particularly good laboratories for evolutionary science because they can be dated accurately using radioactive isotope decay and because they start out as lifeless masses of rock emerging from the sea.
The development of ecosystems on volcanic islands is somewhat unpredictable. However, ecological succession does occur first with pioneer organisms that gradually alter the environment until a stable climax community is established. What is unpredictable is what plant and animal species will colonize these new environments.
Much of this is left to climate, proximity to other land masses, and of course, chance. This investigation deals with three species of lizards of the genus Gallotiaand within one of these species, Gallotia gallotifour separate island populations. The arrival of the Gallotia lizards was probably by rafting See Map 1.
Rafts of natural vegetation are often washed out to sea when high river levels cause river banks to collapse, carrying away both plants and clinging animals. Oceanic currents in this region vary with the seasons.
Colonization by airborne organisms, such as insects and birds, usually occurs during storms. In any case, there are some general principles of island colonization: 1 The closer the island to another land mass, the higher the probability of colonization. What is the phylogenetic history of the three species and seven populations of Gallotia lizards on the Canary Islands?
Does the presence of four morphologically different populations of G. In this investigation, you will use data from geography, geological history, morphology body sizeand molecular genetics to develop answers to these questions. List these distances on a separate page. Return to top 1 Which island is most likely to have been colonized first and which last?
Tell why you think so. Your teacher will demonstrate how to draw a phylogenetic tree. The maximum age of each island was estimated by sampling volcanic rocks found on all islands. The ratio of radioactive potassium to its breakdown product, argon, was used to estimate the age of the rocks.
Table 1. Maximum age of the Canary Islands in millions of years. Anguita et al. Or what changes should you make and why?A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Syst Biol. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. Models of nucleotide substitution allow for the calculation of probabilities of change between nucleotides along the branches of a phylogenetic tree. The use of a particular substitution model may change the outcome of the phylogenetic analysis e.
In-depth reviews about model selection in phylogenetics are available elsewhere Johnson and Omland ; Posada and Buckley ; Sullivan and Joyce Indeed, the performance of different model selection strategies has been the subject of active research Posada ; Posada and Crandall ; Pol ; Abdo et al.
Several programs already exist for the statistical selection of models of nucleotide substitution e. Among these, Modeltest Posada and Crandall has been one of the most popular.
This note describes a new program called jModelTest that supersedes Modeltest in several aspects. N OTE. DT weights are simply the rescaled reciprocal DT scores. This is a gross implementation very likely to change. Basically, this pipeline fig. Posada : to compute Euclidean distances between trees for performance-based model selection.
Alignments are loaded using the ReadSeq library Gilbert Likelihood calculations, including estimates of model parameters and trees, are carried out with Phyml Guindon and Gascuel A custom program called Ted D. Posada is used to compute Euclidean distances between trees for performance-based model selection DTwhereas Consense Felsenstein is used to calculate weighted and strict consensus trees representing model-averaged phylogenies.
Likelihood calculations, including model parameters and tree estimates, are carried out with Phyml Guindon and Gascuel The tree topology used in these calculations can be the same across models fixed or optimized for each one. In all cases, branch lengths are estimated and counted as parameters. The program offers the possibility of defining to a reasonable extent which models are included in the candidate set.
A series of likelihood ratio tests LRTs can be implemented under a particular hierarchy hLRTsin which the user can specify their order, and whether parameters are added forward selection or removed backward selection. Alternatively, the order of the LRTs can be set dynamically dLRTs Posada and Crandallby comparing the current model with the one that is one hypothesis away and provides the largest increase under forward selection or smallest decrease under backward selection in likelihood.
In this case, sample size has to be specified, which by default is approximated as the number of sites in the alignment note that the sample size of an alignment is presently an unknown quantity. For the DT scores, this calculation is not as straightforward, and right now a very gross approach is used instead, where the DT weights are the rescaled reciprocal DT scores.
Confidence intervals CIs can be defined according to the cumulative weights, including a specified fraction of the models. The program can also calculate the relative importance of every parameter of the substitution model and model-averaged estimates of these, using all the models in the candidate set, or a fraction included in a particular CI see Posada and Buckley Indeed, this option is only available when the tree topology has been optimized for every model.Phylogenetics and Reading Phylogenetic Trees
Model-averaged tree of HIV-1 pol sequences. The topology shown is the consensus of 88 ML tree topologies, one for every model, weighted according to the AIC weights.
The numbers on the branches represent uncertainty due to model selection. Model selection is an important issue in statistical phylogenetics, around which some questions still remain open Kelchner and Thomas I want to thank a number of users of Modeltest that had made numerous comments and suggestions through the years. Special thanks to Stephane Guindon for his generous help with Phyml and to John Huelsenbeck for suggesting the stochastic calculation of CIs.Goodreads helps you keep track of books you want to read.
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Preview — Molecular Evolution by Roderic D. The study of evolution at the molecular level has given the subject of evolutionary biology a new significance.
Molecular Evolution — A Phylogenetic Approach.
Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this The study of evolution at the molecular level has given the subject of evolutionary biology a new significance.
In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor.
This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. Get A Copy. Paperbackpages. More Details Original Title.
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Rating details. All Languages. More filters. Sort order. Caesar rated it liked it Apr 22, Russ rated it really liked it Feb 13, Pete rated it really liked it Apr 25, Joe Ward rated it really liked it Jun 26, The plant hormone abscisic acid ABA plays a crucial role during the plant life cycle as well as in adaptive responses to environmental stresses. They act as negative regulators of members of the protein phosphatase type 2C family. Due to the biological importance of PYLs, many researchers have focused on their genetic redundancy and consequent functional divergence.
However, little is understood of their evolution and its impact on the generation of regulatory diversity. In this study, we identify positive selection and functional divergence in PYLs through phylogenetic reconstruction, gene structure and expression pattern analysis, positive selection analysis, functional divergence analysis, and structure comparison.
We found the correlation of desensitization of PYLs under specific modifications in the molecular recognition domain with functional diversification. Hence, an interesting antagonistic co-evolutionary mechanism is proposed for the functional diversification of ABA receptor family proteins.
Plant systematics : a phylogenetic approach
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Search Menu. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. Materials and methods. Results and Discussion. Supplementary data. Author contributions. Competing interests. Oxford Academic. Google Scholar. Mo-Xian Chen. Jian-Hua Zhang. Ge-Fei Hao. Correspondence: gfyang mail. Guang-Fu Yang.
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There are eight chapters, the first three of which provide an introduction to molecular evolution, phylogenetic tree reconstruction, and the evolution of genes and genomes. Chapter 4 introduces the subject of population genetics and describes how gene genealogies can provide insights into the evolutionary history of populations and speciation events. Chapters 5 and 6 provide a more in-depth discussion of the methods by which evolutionary distances are inferred, the construction of phylogenetic trees, and the advantages and disadvantages of the various techniques in use at the present time.
Chapter 7 uses the neutralist—selectionist debate to discuss many other themes in molecular evolution, such as molecular clocks, codon usage and functional constraint. Finally, the last chapter describes the implications and uses of phylogenetic reconstruction for evolutionary biology in general, demonstrating how such analyses can reveal much about the evolution of gene families, host—parasite cospeciation, epidemiology and speciation and extinction rates. I found this chapter particularly informative as it gives a clear impression of how the modern uses of phylogenetic reconstruction have expanded from their original application of examining the relationships between species using gene trees.
It would, however, have been interesting to have seen some discussion of how the authors think the field will evolve in the future.
Each of the above chapters contains a summary, numerous worked examples, and a further reading list. Various terms and techniques are further explored in separate sections of boxed text and these make it easy for the reader to follow the flow of the main text. Indeed its readability is one of the best aspects of the book and as such it will provide an excellent introduction to the subject of molecular evolution for both undergraduates and research students.
I also think it will be useful for other researchers, particularly molecular biologists, who either want to gain an impression of how their data can be used in an evolutionary context, or who actually want to move into the field of molecular evolution. Having been in this position myself I know how difficult it can be to take this initial step if there is no one to give day-to-day advice.
In this regard it is a pity that the book does not provide more information on how to obtain the actual programs used by the authors in their worked examples: a section or appendix providing web-site addresses and ordering information would have be a most useful addition.Looks like you are currently in Russia but have requested a page in the United States site.
Would you like to change to the United States site? Roderick D. PageEdward C. Roderic Dugald Morton Page, known as Rod, is an evolutionary biologist at the University of Glasgow, Scotland, and the author of several books. As of he is professor at the University of Glasgow and was editor of the journal Systematic Biology until the end of Permissions Request permission to reuse content from this site. Undetected location. NO YES. Molecular Evolution: A Phylogenetic Approach.
Selected type: Paperback. Added to Your Shopping Cart. This is a dummy description. The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences.
In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals.
First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility. Table of contents The Archaeology of the Genome. Trees; Genes: Organization, Function and Evolution. Genes in Populations. Measuring Genetic Change. Inferring Molecular Phylogeny.
Models of Molecular Evolution. Applications of Molecular Phylogenetics. Downloads Artwork from the book You may download the artwork from the book here. Features First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Artwork from the book You may download the artwork from the book here.