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Negative Selection and the Neutral Theory of Molecular Evolution

Norman A. Johnson

in Darwinian Detectives: Revealing the Natural History of Genes and Genomes

Published in print:
2007
Published Online:
September 2007
ISBN:
9780195306750
eISBN:
9780199790203
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195306750.003.0003
Subject:
Biology, Evolutionary Biology / Genetics

Natural selection is not the only evolutionary “force” that can alter frequencies of genetic variants; random genetic drift (a sampling process) persistently changes the gene pool of populations, ... More


Basics in Molecular Evolution

Xun Gu

in Statistical Theory and Methods for Evolutionary Genomics

Published in print:
2010
Published Online:
January 2011
ISBN:
9780199213269
eISBN:
9780191594762
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199213269.003.0001
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies

Molecular evolution is the study of the process of evolution at the level of DNA, RNA, and proteins, in which the neutral or nearly neutral evolution model has provided the theoretical basis. Yet, ... More


Advanced Topics in Systems Biology and Network Evolution

Xun Gu

in Statistical Theory and Methods for Evolutionary Genomics

Published in print:
2010
Published Online:
January 2011
ISBN:
9780199213269
eISBN:
9780191594762
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199213269.003.0010
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies

As evolutionary biologists have always been concerned with the genetic basis for the emergence of complex phenotypes, advances in genomics and systems biology are facilitating a paradigm shift of ... More


Natural Selection and Genetic Drift: Their Role in Evolutionary Change

John O. Reiss

in Not by Design: Retiring Darwin's Watchmaker

Published in print:
2009
Published Online:
March 2012
ISBN:
9780520258938
eISBN:
9780520944404
Item type:
chapter
Publisher:
University of California Press
DOI:
10.1525/california/9780520258938.003.0009
Subject:
Biology, Evolutionary Biology / Genetics

This chapter explores the fundamental distinction between natural selection and genetic drift, starting from a consideration of how they are measured, and suggests that it may not be as fundamental ... More


Biodiversity

Kevin J. Gaston

in Conservation Biology for All

Published in print:
2010
Published Online:
February 2010
ISBN:
9780199554232
eISBN:
9780191720666
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199554232.003.0003
Subject:
Biology, Ecology, Biodiversity / Conservation Biology

Kevin J. Gaston defines biodiversity and lays out obstacles to its better understanding in this chapter. Biodiversity is the variety of life in all of its many manifestations. This variety can ... More


Detecting Positive Selection

Norman A. Johnson

in Darwinian Detectives: Revealing the Natural History of Genes and Genomes

Published in print:
2007
Published Online:
September 2007
ISBN:
9780195306750
eISBN:
9780199790203
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195306750.003.0004
Subject:
Biology, Evolutionary Biology / Genetics

Positive natural selection, though rare in comparison with negative selection, is the main evolutionary force responsible for adaptive evolutionary change. Using the neutral theory to generate null ... More


Molecular Evolution: A Statistical Approach

Ziheng Yang

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199602605
eISBN:
9780191782251
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199602605.001.0001
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This book summarizes the statistical models and computational algorithms for comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, and ... More


High-Dimensional Adaptive Landscapes Facilitate Evolutionary Innovation

Andreas Wagner

in The Adaptive Landscape in Evolutionary Biology

Published in print:
2013
Published Online:
December 2013
ISBN:
9780199595372
eISBN:
9780191774799
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199595372.003.0017
Subject:
Biology, Evolutionary Biology / Genetics

High-dimensional adaptive landscapes facilitate the origin of evolutionary adaptations and innovations, qualitatively new and beneficial phenotypes. This chapter discusses evidence for this assertion ... More


Simulating molecular evolution

ZIHENG YANG

in Computational Molecular Evolution

Published in print:
2006
Published Online:
April 2010
ISBN:
9780198567028
eISBN:
9780191728280
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198567028.003.0009
Subject:
Biology, Evolutionary Biology / Genetics

This chapter discusses basic techniques of computer simulation. Topics covered include random number generator, generation of continuous random variables, generation of discrete random variables, and ... More


Integrating Genomics into Evolutionary Theory

Gregory A. Wray

in Evolution—the Extended Synthesis

Published in print:
2010
Published Online:
August 2013
ISBN:
9780262513678
eISBN:
9780262315142
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262513678.003.0005
Subject:
Biology, Evolutionary Biology / Genetics

This chapter characterizes the consequences of a shift of focus from individual genes to gene networks. It describes some of the opportunities and challenges that the genomic era brings to ... More


The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence

Belinda S. W. Chang, Jingjing Du, Cameron J. Weadick, Johannes Müller, Constanze Bickelmann, D. David Yu, and James M. Morrow

in Codon Evolution: Mechanisms and Models

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199601165
eISBN:
9780191810114
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199601165.003.0011
Subject:
Biology, Evolutionary Biology / Genetics

This chapter focuses on the use of codon models for ancestral sequence reconstruction, and for use in clade models of functional divergence. It first reviews codon-based ancestral reconstruction ... More


Bayesian methods

ZIHENG YANG

in Computational Molecular Evolution

Published in print:
2006
Published Online:
April 2010
ISBN:
9780198567028
eISBN:
9780191728280
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198567028.003.0005
Subject:
Biology, Evolutionary Biology / Genetics

This chapter provides a brief introduction to the theory and computation of Bayesian statistics and its applications to molecular evolution. It uses simple examples, such as distance estimation under ... More


Hemoglobin: Insights into protein structure, function, and evolution

Jay F. Storz

Published in print:
2018
Published Online:
December 2018
ISBN:
9780198810681
eISBN:
9780191847929
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198810681.001.0001
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

The aims of this book are to provide a synthesis of our current understanding of hemoglobin structure, function, and evolution, and to illustrate how research on this paradigmatic protein has ... More


Rolling the Dice Twice: Evolving Reconstructed Ancient Proteins in Extant Organisms

Betul Kacar

in Chance in Evolution

Published in print:
2016
Published Online:
May 2017
ISBN:
9780226401744
eISBN:
9780226401911
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226401911.003.0012
Subject:
Philosophy, Philosophy of Science

Scientists have access to artifacts of evolutionary history, but they have limited ability to infer the exact events that produced today’s living world. An intriguing question to arise from this ... More


Toward living nanomachines

Christof Mast, Friederike Möller, Moritz Kreysing, Severin Schink, Benedikt Obermayer, Ulrich Gerland, and Dieter Braun

in Living machines: A handbook of research in biomimetics and biohybrid systems

Published in print:
2018
Published Online:
June 2018
ISBN:
9780199674923
eISBN:
9780191842702
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780199674923.003.0039
Subject:
Neuroscience, Sensory and Motor Systems, Development

How does inanimate matter become transformed into animate matter? Living systems evolve by replication and selection at the molecular level and this chapter considers how to establish a synthetic, ... More


Simulating molecular evolution

Ziheng Yang

in Molecular Evolution: A Statistical Approach

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199602605
eISBN:
9780191782251
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199602605.003.0012
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This chapter introduces computer simulation and in particular simulation of the molecular evolutionary process. It covers the generation of random numbers as well as other discrete and continuous ... More


Evolution and Selection of Quantitative Traits

Bruce Walsh and Michael Lynch

Published in print:
2018
Published Online:
September 2018
ISBN:
9780198830870
eISBN:
9780191868986
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830870.001.0001
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show ... More


Background

Adrian Schneider and Gina M. Cannarozzi

in Codon Evolution: Mechanisms and Models

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199601165
eISBN:
9780191810114
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199601165.003.0001
Subject:
Biology, Evolutionary Biology / Genetics

This background chapter summarizes some of the basic concepts used in molecular evolution, such as the use of Markov models in modelling sequence evolution as well as maximum-likelihood and Bayesian ... More


Introduction

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0001
Subject:
Mathematics, Mathematical Biology

This introductory chapter first discusses the molecular evolution and the birth of the combinatorics of genome rearrangements. It then describes the genome rearrangement problem; the scope of the ... More


Declines of Eastern North American Woodland Salamanders (Plethodon)

Richard Highton

in Amphibian Declines: The Conservation Status of United States Species

Published in print:
2005
Published Online:
March 2012
ISBN:
9780520235922
eISBN:
9780520929432
Item type:
chapter
Publisher:
University of California Press
DOI:
10.1525/california/9780520235922.003.0008
Subject:
Biology, Animal Biology

Recent declines and extinctions of amphibian populations have been reported in many areas of the world. A majority of the documented declines are in easily detectable anuran species, including ... More


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