Phylogenetic Comparative Methods in R

Biology

Phylogenetic Comparative Methods in R

Liam J. Revell and Luke J. Harmon

An authoritative introduction to the latest comparative methods in evolutionary biology

Hardcover

Price:: $165.00/拢138.00
ISBN:
Published (US):: Sep 6, 2022
Published (UK):: Sep 27, 2022
Copyright:: 2022
Pages:: 440
Size:: 8 x 10 in.
Illus:: 136 b/w illus.
Main_subject:: Biology

Paperback

Price:: $165.00/拢138.00
ISBN:
Published (US):: Sep 6, 2022
Published (UK):: Sep 27, 2022
Copyright:: 2022
Pages:: 440
Size:: 8 x 10 in.
Illus:: 136 b/w illus.
Main_subject:: Biology

ebook

Price:: $165.00/拢138.00
ISBN:
Published (US):: Sep 6, 2022
Published (UK):: Sep 27, 2022
Copyright:: 2022
Pages:: 440
Size:: 8 x 10 in.
Illus:: 136 b/w illus.
Main_subject:: Biology

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Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life.

Covers every major method of modern phylogenetic comparative analysis in R
Explains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualization
Features a wealth of exercises and challenge problems
Serves as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areas
Written by two of today鈥檚 leading developers of phylogenetic comparative methods

Liam J. Revell is associate professor of biology at the University of Massachusetts, Boston, and an adjunct researcher at the Universidad Cat贸lica de la Sant铆sima Concepci贸n in Chile. Luke J. Harmon is professor of biological sciences at the University of Idaho and the author of Phylogenetic Comparative Methods: Learning from Trees.

1 A brief introduction to phylogenetics in R
- 1.1 Introduction
- 1.2 Preliminaries
- 1.3 R phylogenetics
- 1.4 ape and the 鈥減hylo鈥� object in R
- 1.5 The internal structure of a tree in R
- 1.6 Reading and writing phylogenetic trees
- 1.7 Plotting and manipulating trees
- 1.8 Multiple trees in a single object
- 1.9 Managing trees and comparative data
- 1.10 A simple comparative analysis: Phylogenetic principal components analysis
- 1.11 Practice problems

2 Phylogenetically independent contrasts
- 2.1 Introduction
- 2.2 Phylogenetic nonindependence
- 2.3 Phylogenetically independent contrasts
- 2.4 What happens if we ignore the tree?
- 2.5 Practice problems

3 Phylogenetic generalized least squares
- 3.1 Introduction
- 3.2 Statistical nonindependence of phylogenetic data
- 3.3 Equivalence of contrasts regression and PGLS
- 3.4 Assumptions of PGLS
- 3.5 Phylogenetic ANOVA and ANCOVA
- 3.6 Practice problems

4 Modeling continuous character evolution on a phylogeny
- 4.1 Introduction
- 4.2 The Brownian motion model
- 4.3 Brownian motion on a phylogeny
- 4.4 Properties of Brownian motion
- 4.5 Fitting a Brownian model to data
- 4.6 Phylogenetic signal
- 4.7 Other models of continuous character evolution on phylogenies
- 4.8 Fitting and comparing alternative continuous character models
- 4.9 Practice problems

5 Multi-rate, multi-regime, and multivariate models for continuous traits
- 5.1 Multi-rate Brownian evolution
- 5.2 Multi-optimum Ornstein鈥揢hlenbeck evolution
- 5.3 Multivariate Brownian evolution
- 5.4 Exploring evolutionary heterogeneity
- 5.5 Practice problems

6 Modeling discrete character evolution on a phylogeny
- 6.1 Introduction
- 6.2 The Mk model
- 6.3 Fitting the Mk model to data
- 6.4 Comparing alternative discrete character models
- 6.5 Practice problems

7 Other models of discrete character evolution
- 7.1 Introduction
- 7.2 Correlated binary traits
- 7.3 Modeling heterogeneity in the evolutionary rate for a discrete trait
- 7.4 Modeling rate variation using the hidden-rates model
- 7.5 A polymorphic trait model
- 7.6 The threshold model for studying discrete and continuous character traits
- 7.7 Practice problems

8 Reconstructing ancestral states
- 8.1 Introduction
- 8.2 Ancestral states for continuous characters
- 8.3 Properties of ancestral state estimation for continuous traits
- 8.4 Discrete characters
- 8.5 Joint ancestral state reconstruction
- 8.6 Marginal ancestral state reconstruction
- 8.7 Stochastic character mapping
- 8.8 What about parsimony?
- 8.9 Practice problems

9 Analysis of diversification with phylogenies
- 9.1 Introduction
- 9.2 Lineage-through-time plots and the 螕 statistic
- 9.3 Estimating speciation and extinction rates from a reconstructed phylogeny
- 9.4 The effect of incomplete sampling on diversification rates
- 9.5 Likelihood surface of a birth-death model
- 9.6 Analyzing diversification using diversitree
- 9.7 Practice problems

10 Time- and density-dependent diversification
- 10.1 Introduction
- 10.2 Time-varying diversification
- 10.3 Fitting time-variable diversification models to data
- 10.4 Diversity-dependent diversification
- 10.5 Testing for variation in diversification rates among clades
- 10.6 Practice problems

11 Character-dependent diversification
- 11.1 Introduction
- 11.2 Binary-state speciation and extinction (BiSSE) model
- 11.3 Multi-state speciation and extinction (MuSSE) model
- 11.4 Hidden-state speciation and extinction (HiSSE) model
- 11.5 Quantitative-trait speciation and extinction (QuaSSE) model
- 11.6 Practice problems

12 Biogeography and phylogenetic community ecology
- 12.1 Introduction
- 12.2 Ancestral area reconstruction
- 12.3 Phylogenetic community ecology
- 12.4 Practice problems

13 Plotting phylogenies and comparative data
- 13.1 Introduction
- 13.2 Phylogenies in the R plotting environment
- 13.3 Plotting phylogenies without actually plotting them
- 13.4 Algorithms for drawing trees
- 13.5 Practice problems

References
Index
Index of R functions

鈥淩evell and Harmon have played a leading role not only in developing new phylogenetic and comparative methods but in providing the means for us mere mortals to use them. This book is a must-have for anyone working in comparative biology.鈥濃€擩onathan B. Losos, editor in chief of The Princeton Guide to Evolution

鈥淩evell and Harmon provide effective tutorials on key phylogenetic comparative methods in R, and the skills users will develop from working through this book are highly transferable to a vast range of other techniques in the biological sciences. The field of phylogenetic comparative biology is fast-moving and there is a need for a practical handbook such as this.鈥濃€擲ally Street, Durham University

鈥淭his comprehensive guide to comparative methods in R will surely be a resource for any newcomer to using phylogenies. The range of sample data sets is exceptional and gives readers the ability to interpret results from different perspectives. Revell and Harmon鈥檚 book is an excellent resource for any graduate student interested in delving into comparative methods for their thesis work.鈥濃€擩eremy Beaulieu, University of Arkansas

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Phylogenetic Comparative Methods in R

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