Phylogenetic Comparative Methods

by Luke Harmon

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Evolution is happening all around us. In many cases – lately, due to technological advances in molecular biology – scientists can now describe the evolutionary process in exquisite detail. We understand the genetics, development, and biomechanical processes that link changes in a Galapagos finches’ diet to the shape of their bill. And, in some cases, we can watch as one species splits to become two.

Description from LibreTexts.

Publisher
University of Idaho
Subjects
Biology, Evolutionary Developmental Biology
Licence
CC BY 4.0, as LibreTexts states it
Who can read
Tweens profiles and older, judged from its title and subjects

Contents

LibreTexts writes equations in TeX, and here they show as TeX; the PDF has them typeset.

  1. Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. 1: A Macroevolutionary Research Program
  7. 1.1: Introduction
  8. 1.2: The roots of comparative methods
  9. 1.3: A brief Introduction to Phylogenetic Trees
  10. 1.4: What we can (and can’t) learn about evolutionary history from living species
  11. 1.5: Overview of the book
  12. 1.S: A Macroevolutionary Research Program (Summary)
  13. 2: Fitting Statistical Models to Data
  14. 2.1: Introduction
  15. 2.2: Standard Statistical Hypothesis Testing
  16. 2.3: Maximum Likelihood
  17. 2.4: Bayesian Statistics
  18. 2.5: AIC versus Bayes
  19. 2.6: Models and Comparative Methods
  20. 2.S: Fitting Statistical Models to Data (Summary)
  21. 3: Introduction to Brownian Motion
  22. 3.1: Introduction to Brownian Motion
  23. 3.2: Properties of Brownian Motion
  24. 3.3: Simple Quantitative Genetics Models for Brownian Motion
  25. 3.4: Brownian Motion on a Phylogenetic Tree
  26. 3.5: Multivariate Brownian motion
  27. 3.6: Simulating Brownian motion on trees
  28. 3.S: Introduction to Brownian Motion (Summary)
  29. 4: Fitting Brownian Motion
  30. 4.1: Introduction
  31. 4.2: Estimating Rates using Independent Contrasts
  32. 4.3: Estimating rates using maximum likelihood
  33. 4.4: Bayesian approach to evolutionary rates
  34. 4.5: Summary
  35. 5: Multivariate Brownian Motion
  36. 5.1: Introduction to Multivariate Brownian Motion
  37. 5.2: What is evolutionary correlation?
  38. 5.3: Modeling the evolution of correlated characters
  39. 5.4: Testing for evolutionary correlations
  40. 5.5: Multivariate Brownian Motion (Summary)
  41. 6: Beyond Brownian Motion
  42. 6.1: Introduction to Non-Brownian Motion
  43. 6.2: Transforming the evolutionary variance-covariance matrix
  44. 6.3: Variation in rates of trait evolution across clades
  45. 6.4: Non-Brownian evolution under stabilizing selection
  46. 6.5: Early Burst Models
  47. 6.6: Peak Shift Models
  48. 6.7: Appendix - Deriving an OU model under stabilizing selection
  49. 6.S: Beyond Brownian Motion (Summary)
  50. 7: Models of Discrete Character Evolution
  51. 7.1: Limblessness as a discrete trait
  52. 7.2: Modeling the evolution of discrete states
  53. 7.3: The Mk Model
  54. 7.4: The Extended Mk Model
  55. 7.5: Simulating the Mk model on a tree
  56. 7.6: R Markdown to Recreate Analyses
  57. 7.S: Models of Discrete Character Evolution (Summary)
  58. 8: Fitting Models of Discrete Character Evolution
  59. 8.1: The Evolution of Limbs and Limblessness
  60. 8.2: Fitting Mk models to Comparative Data
  61. 8.3: Using Maximum likelihood to Estimate Parameters of the Mk model
  62. 8.4: Using Bayesian MCMC to estimate parameters of the Mk model
  63. 8.5: Exploring Mk - the "total garbage" test
  64. 8.6: Testing for Differences in the Forwards and Backwards Rate of Character Change
  65. 8.7: Appendix - Felsenstein's Pruning Algorithm
  66. 8.S: Fitting models of discrete character evolution (Summary)
  67. 9: Beyond the Mk Model
  68. 9.1: The Evolution of Frog Life History Strategies
  69. 9.2: Beyond the Mk model
  70. 9.3: Pagel’s λ, δ, and κ
  71. 9.4: Mk models where parameters vary across clades and/or through time
  72. 9.5: Threshold Models
  73. 9.6: Modeling more than one Discrete Character at a Time
  74. 9.7: Testing for non-independent evolution of different characters
  75. 9.S: Beyond the Mk Model (Summary)
  76. 10: Introduction to Birth-Death Models
  77. 10.1: Plant Diversity Imbalance
  78. 10.2: The Birth-Death Model
  79. 10.3: Birth-death models and phylogenetic trees
  80. 10.4: Simulating Birth-Death Trees
  81. 10.5: Tree topology, tree shape, and tree balance under a birth-death model
  82. 10.6: Lineage-through-Time Plots
  83. 10.S: Introduction to birth-death models (Summary)
  84. 11: Fitting Birth-Death Models
  85. 11.1: Hotspots of Diversity
  86. 11.2: Clade Age and Diversity
  87. 11.3: Tree Balance
  88. 11.4: Fitting birth-death models to branching times
  89. 11.5: Sampling and birth-death models
  90. 11.S: Fitting Birth-Death Models (Summary)
  91. 12: Beyond Birth-Death models
  92. 12.1: Capturing Variable Evolution
  93. 12.2: Variation in Diversification Rates across Clades
  94. 12.3: Variation in Diversification Rates through Time
  95. 12.4: Diversity-Dependent Models
  96. 12.5: Protracted Speciation
  97. 12.S: Beyond Birth-Death Models (Summary)
  98. 13: Characters and Diversification Rates
  99. 13.1: The Evolution of Self-Incompatibility
  100. 13.2: A State-Dependent Model of Diversification
  101. 13.3: Calculating Likelihoods for State-Dependent Diversification Models
  102. 13.4: ML and Bayesian Tests for State-Dependent Diversification
  103. 13.5: Potential Pitfalls and How to Avoid Them
  104. 13.S: Characters and Diversification Rates (Summary)
  105. 14: What have we learned from the trees?
  106. 14.1: The Lorax
  107. 14.2: What We Have Learned so Far
  108. 14.3: Where Can we go Next?
  109. 14.4: A hint at the future of comparative methods
  110. 14.S: What have we learned from the trees? (Summary)
  111. Back Matter
  112. Index
  113. Glossary
  114. Detailed Licensing