Phylogenetic Comparative Methods in R

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Beschreibung

An authoritative introduction to the latest comparative methods in evolutionary biology

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's leading developers of phylogenetic comparative methods

Über den Autor

Liam J. Revell is associate professor of biology at the University of Massachusetts, Boston, and an adjunct researcher at the Universidad Católica de la Santísima Concepción 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.

Inhaltsverzeichnis

1 A brief introduction to phylogenetics in R
- 1.1 Introduction
- 1.2 Preliminaries
- 1.3 R phylogenetics
- 1.4 ape and the “phylo” 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-Uhlenbeck 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 Γ 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

Details

Erscheinungsjahr:	2022
Genre:	Biologie , Importe
Rubrik:	Naturwissenschaften & Technik
Medium:	Taschenbuch
Inhalt:	Einband - flex.(Paperback)
ISBN-13:	9780691219035
ISBN-10:	0691219036
Sprache:	Englisch
Einband:	Kartoniert / Broschiert
Autor:	Revell, Liam J. Harmon, Luke J.
Hersteller:	Princeton University Press
Verantwortliche Person für die EU:	Libri GmbH, Europaallee 1, D-36244 Bad Hersfeld, gpsr@libri.de
Maße:	254 x 203 x 24 mm
Von/Mit:	Liam J. Revell (u. a.)
Erscheinungsdatum:	06.09.2022
Gewicht:	0,937 kg