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Evolution in Time

Michael Heads

in Molecular Panbiogeography of the Tropics

Published in print:
2012
Published Online:
September 2012
ISBN:
9780520271968
eISBN:
9780520951808
Item type:
chapter
Publisher:
University of California Press
DOI:
10.1525/california/9780520271968.003.0002
Subject:
Biology, Evolutionary Biology / Genetics

The idea of an evolutionary clock can be rejected, along with its derivative, the molecular clock. The time course of a phylogeny can be calibrated using fossils, age of islands or strata that ... More


Molecular clock and estimation of species divergence times

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/9780198567028.003.0007
Subject:
Biology, Evolutionary Biology / Genetics

This chapter focuses on statistical methods for testing the clock hypothesis, and on likelihood and Bayesian methods for dating species divergence events under global and local clock models. In such ... More


The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

Kevin J. Peterson, James A. Cotton, James G. Gehling, and Davide Pisani

in Animal Evolution: Genomes, Fossils, and Trees

Published in print:
2009
Published Online:
September 2009
ISBN:
9780199549429
eISBN:
9780191721601
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199549429.003.0002
Subject:
Biology, Evolutionary Biology / Genetics, Developmental Biology

Unraveling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times ... More


Animal phylogenetics

Alessandro Minelli

in Perspectives in Animal Phylogeny and Evolution

Published in print:
2008
Published Online:
May 2009
ISBN:
9780198566205
eISBN:
9780191713866
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198566205.003.0002
Subject:
Biology, Animal Biology, Evolutionary Biology / Genetics

The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially ... More


Molecular clock and estimation of species divergence times

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/9780199602605.003.0010
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This chapter discusses the hypothesis of the molecular clock and its use to date species divergences. It introduces various tests of the molecular clock as well as strategies to relax the clock in ... More


Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling

Eric A. Gaucher

in Ancestral Sequence Reconstruction

Published in print:
2007
Published Online:
September 2008
ISBN:
9780199299188
eISBN:
9780191714979
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199299188.003.0002
Subject:
Biology, Evolutionary Biology / Genetics

The perspective on natural history and medicine by Emile Zuckerkandl combined with the chemical expertise of Linus Pauling generated many novel ideas concerning molecular evolution. These included ... More


The earliest fossil record of the animals and its significance

Graham E. Budd

in Animal Evolution: Genomes, Fossils, and Trees

Published in print:
2009
Published Online:
September 2009
ISBN:
9780199549429
eISBN:
9780191721601
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199549429.003.0001
Subject:
Biology, Evolutionary Biology / Genetics, Developmental Biology

The fossil record of the earliest animals has been enlivened in recent years by a series of spectacular discoveries, including embryos, from the Ediacaran to the Cambrian, but many issues, not least ... More


Morphology and Molecules: An Integrated Comparison of Phenotypic and Genetic Rates of Evolution

Steven J. Hageman

in Species and Speciation in the Fossil Record

Published in print:
2016
Published Online:
May 2017
ISBN:
9780226377445
eISBN:
9780226377582
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226377582.003.0006
Subject:
Biology, Paleontology: Biology

Our understanding of processes that contribute to the origin of species is informed by the study of phenotypic variation (morphology) through geologic time and broader phenotypes of living organisms ... 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


When did eukaryotes evolve?

Tim Lenton and Andrew Watson

in Revolutions that made the Earth

Published in print:
2011
Published Online:
December 2013
ISBN:
9780199587049
eISBN:
9780191775031
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199587049.003.0012
Subject:
Physics, Geophysics, Atmospheric and Environmental Physics

This chapter discusses the three main techniques for recognising when eukaryotes first appeared. Each technique, however, gives different answers, with its own set of problems. The most obvious ... More


Understanding Molecular Clocks and Time Trees

Andrew V. Z. Brower and Randall T. Schuh

in Biological Systematics: Principles and Applications

Published in print:
2021
Published Online:
September 2021
ISBN:
9781501752773
eISBN:
9781501752797
Item type:
chapter
Publisher:
Cornell University Press
DOI:
10.7591/cornell/9781501752773.003.0011
Subject:
Biology, Biochemistry / Molecular Biology

This chapter examines molecular clocks and time trees. Although laden with numerous process assumptions that may or may not be true (or knowable), the idea is appealingly straightforward: if amino ... More


Molecular Population Genetics

Daniel L. Hartl

in A Primer of Population Genetics and Genomics

Published in print:
2020
Published Online:
August 2020
ISBN:
9780198862291
eISBN:
9780191895074
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198862291.003.0007
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

Chapter 7 is an introduction to molecular population genetics that includes the principal concepts of nucleotide polymorphism and divergence, the site frequency spectrum, and tests of selection and ... More


Neutral theories of molecular evolution

Asher D. Cutter

in A Primer of Molecular Population Genetics

Published in print:
2019
Published Online:
August 2019
ISBN:
9780198838944
eISBN:
9780191874826
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198838944.003.0004
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

Chapter 4, “Neutral theories of molecular evolution,” outlines the logic and predictions of the neutral theory of molecular evolution and its derivatives as a simple conceptual framework for ... More


Inferring evolutionary processes from DNA sequence data

Glenn-Peter Sætre and Mark Ravinet

in Evolutionary Genetics: Concepts, Analysis, and Practice

Published in print:
2019
Published Online:
July 2019
ISBN:
9780198830917
eISBN:
9780191868993
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830917.003.0007
Subject:
Biology, Evolutionary Biology / Genetics, Biomathematics / Statistics and Data Analysis / Complexity Studies

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if ... More


Use of codon models in molecular dating and functional analysis

Steven A. Benner

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/9780199601165.003.0010
Subject:
Biology, Evolutionary Biology / Genetics

This chapter focuses on the use of codon models for molecular dating and functional analysis, with a critical view on the actual usefulness of models on practical problems. According to Darwinian ... More


Biological Systematics: Principles and Applications

Andrew V. Z. Brower and Randall T. Schuh

Published in print:
2021
Published Online:
September 2021
ISBN:
9781501752773
eISBN:
9781501752797
Item type:
book
Publisher:
Cornell University Press
DOI:
10.7591/cornell/9781501752773.001.0001
Subject:
Biology, Biochemistry / Molecular Biology

Understanding the history and philosophy of biological systematics (phylogenetics, taxonomy and classification of living things) is key to successful practice of the discipline. In this thoroughly ... More


Nature’s green revolution

David Beerling

in The Emerald Planet: How plants changed Earth's history

Published in print:
2007
Published Online:
November 2020
ISBN:
9780192806024
eISBN:
9780191916427
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780192806024.003.0015
Subject:
Earth Sciences and Geography, Environmental Geography

The scientific revolution of the seventeenth and eighteenth centuries, if indeed it can be recognized as such, saw the foundations of modern science established. Developments by iconic figures, ... More


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