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Using phylogeny to understand genomic evolution

David A. Liberles

in Parsimony, Phylogeny, and Genomics

Published in print:
2006
Published Online:
September 2007
ISBN:
9780199297306
eISBN:
9780191713729
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199297306.003.0010
Subject:
Biology, Evolutionary Biology / Genetics

As genome sequencing projects have propagated, comparative genomics has emerged as a method of choice for understanding protein function. There are simple approaches for comparing sequences, like ... More


Dollo parsimony and the reconstruction of genome evolution

Igor B. Rogozin, Yuri I. Wolf, Vladimir N. Babenko, and Eugene V. Koonin

in Parsimony, Phylogeny, and Genomics

Published in print:
2006
Published Online:
September 2007
ISBN:
9780199297306
eISBN:
9780191713729
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199297306.003.0011
Subject:
Biology, Evolutionary Biology / Genetics

The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to ... More


Maximum likelihood methods

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/9780199602605.003.0004
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This chapter describes the pruning algorithm for calculating the likelihood on a tree, as well as extensions under complex substitution models, including the gamma and covarion models of rate ... More


Detecting Patterns of Trait Evolution

Marc W. Cadotte and T. Jonathan Davies

in Phylogenies in Ecology: A Guide to Concepts and Methods

Published in print:
2016
Published Online:
January 2018
ISBN:
9780691157689
eISBN:
9781400881192
Item type:
chapter
Publisher:
Princeton University Press
DOI:
10.23943/princeton/9780691157689.003.0005
Subject:
Biology, Ecology

This chapter examines a variety of methods for detecting the patterns of evolution of a certain trait. It first considers common metrics for evaluating phylogenetic signal and compares fit of ... More


Evolutionary Transitions in Mode of Development

Rachel Collin and Amy Moran (eds)

in Evolutionary Ecology of Marine Invertebrate Larvae

Published in print:
2017
Published Online:
January 2018
ISBN:
9780198786962
eISBN:
9780191829086
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198786962.003.0004
Subject:
Biology, Aquatic Biology, Ecology

In the large body of literature on ecological and evolutionary mechanisms underlying transitions between planktotrophy and lecithotrophy, the focus has typically covered long evolutionary timescales; ... More


Classification, Phylogeny, and Anatomical Evolution of Palms

P. Barry Tomlinson, James W. Horn, and Jack B. Fisher

in The Anatomy of Palms: Arecaceae - Palmae

Published in print:
2011
Published Online:
May 2015
ISBN:
9780199558926
eISBN:
9780191810077
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199558926.003.0009
Subject:
Biology, Plant Sciences and Forestry

This book attempts to reconstruct the evolutionary history of anatomical characters to which previous studies attributed systematic significance, as well as to highlight the systematic significance ... More


Evolutionary origins and diversification of mutualism

George D. Weiblen and Erin L. Treiber

in Mutualism

Published in print:
2015
Published Online:
September 2015
ISBN:
9780199675654
eISBN:
9780191809422
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199675654.003.0003
Subject:
Biology, Ecology, Evolutionary Biology / Genetics

Investigating the past may shed light on evolutionary processes influencing the origin and diversification of mutualism. Evidence from a broad spectrum of species interactions suggests that mutualism ... More


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