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Phylogenetic Comparative Methods

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Phylogenetic Comparative Methods

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.

Evolutionary Developmental BiologyBiology
Author
Luke Harmon
Publisher
University of Idaho
Source
LibreTexts
License
CC BY
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 105 sections
  1. 01: A Macroevolutionary Research Program
  2. 1.0S: 1.S: A Macroevolutionary Research Program (Summary)
  3. 1.01: Introduction
  4. 1.02: The roots of comparative methods
  5. 1.03: A brief Introduction to Phylogenetic Trees
  6. 1.04: What we can (and can’t) learn about evolutionary history from living species
  7. 1.05: Overview of the book
  8. 02: Fitting Statistical Models to Data
  9. 2.0S: 2.S: Fitting Statistical Models to Data (Summary)
  10. 2.01: Introduction
  11. 2.02: Standard Statistical Hypothesis Testing
  12. 2.03: Maximum Likelihood
  13. 2.04: Bayesian Statistics
  14. 2.05: AIC versus Bayes
  15. 2.06: Models and Comparative Methods
  16. 03: Introduction to Brownian Motion
  17. 3.0S: 3.S: Introduction to Brownian Motion (Summary)
  18. 3.01: Introduction to Brownian Motion
  19. 3.02: Properties of Brownian Motion
  20. 3.03: Simple Quantitative Genetics Models for Brownian Motion
  21. 3.04: Brownian Motion on a Phylogenetic Tree
  22. 3.05: Multivariate Brownian motion
  23. 3.06: Simulating Brownian motion on trees
  24. 04: Fitting Brownian Motion
  25. 4.01: Introduction
  26. 4.02: Estimating Rates using Independent Contrasts
  27. 4.03: Estimating rates using maximum likelihood
  28. 4.04: Bayesian approach to evolutionary rates
  29. 4.05: Summary
  30. 05: Multivariate Brownian Motion
  31. 5.01: Introduction to Multivariate Brownian Motion
  32. 5.02: What is evolutionary correlation?
  33. 5.03: Modeling the evolution of correlated characters
  34. 5.04: Testing for evolutionary correlations
  35. 5.05: Multivariate Brownian Motion (Summary)
  36. 06: Beyond Brownian Motion
  37. 6.0S: 6.S: Beyond Brownian Motion (Summary)
  38. 6.01: Introduction to Non-Brownian Motion
  39. 6.02: Transforming the evolutionary variance-covariance matrix
  40. 6.03: Variation in rates of trait evolution across clades
  41. 6.04: Non-Brownian evolution under stabilizing selection
  42. 6.05: Early Burst Models
  43. 6.06: Peak Shift Models
  44. 6.07: Appendix - Deriving an OU model under stabilizing selection
  45. 07: Models of Discrete Character Evolution
  46. 7.0S: 7.S: Models of Discrete Character Evolution (Summary)
  47. 7.01: Limblessness as a discrete trait
  48. 7.02: Modeling the evolution of discrete states
  49. 7.03: The Mk Model
  50. 7.04: The Extended Mk Model
  51. 7.05: Simulating the Mk model on a tree
  52. 7.06: R Markdown to Recreate Analyses
  53. 08: Fitting Models of Discrete Character Evolution
  54. 8.0S: 8.S: Fitting models of discrete character evolution (Summary)
  55. 8.01: The Evolution of Limbs and Limblessness
  56. 8.02: Fitting Mk models to Comparative Data
  57. 8.03: Using Maximum likelihood to Estimate Parameters of the Mk model
  58. 8.04: Using Bayesian MCMC to estimate parameters of the Mk model
  59. 8.05: Exploring Mk - the "total garbage" test
  60. 8.06: Testing for Differences in the Forwards and Backwards Rate of Character Change
  61. 8.07: Appendix - Felsenstein's Pruning Algorithm
  62. 09: Beyond the Mk Model
  63. 9.0S: 9.S: Beyond the Mk Model (Summary)
  64. 9.01: The Evolution of Frog Life History Strategies
  65. 9.02: Beyond the Mk model
  66. 9.03: Pagel’s λ, δ, and κ
  67. or through time
  68. 9.05: Threshold Models
  69. 9.06: Modeling more than one Discrete Character at a Time
  70. 9.07: Testing for non-independent evolution of different characters
  71. 10: Introduction to Birth-Death Models
  72. 10.0S: 10.S: Introduction to birth-death models (Summary)
  73. 10.01: Plant Diversity Imbalance
  74. 10.02: The Birth-Death Model
  75. 10.03: Birth-death models and phylogenetic trees
  76. 10.04: Simulating Birth-Death Trees
  77. 10.05: Tree topology, tree shape, and tree balance under a birth-death model
  78. 10.06: Lineage-through-Time Plots
  79. 11: Fitting Birth-Death Models
  80. 11.0S: 11.S: Fitting Birth-Death Models (Summary)
  81. 11.01: Hotspots of Diversity
  82. 11.02: Clade Age and Diversity
  83. 11.03: Tree Balance
  84. 11.04: Fitting birth-death models to branching times
  85. 11.05: Sampling and birth-death models
  86. 12: Beyond Birth-Death models
  87. 12.0S: 12.S: Beyond Birth-Death Models (Summary)
  88. 12.01: Capturing Variable Evolution
  89. 12.02: Variation in Diversification Rates across Clades
  90. 12.03: Variation in Diversification Rates through Time
  91. 12.04: Diversity-Dependent Models
  92. 12.05: Protracted Speciation
  93. 13: Characters and Diversification Rates
  94. 13.0S: 13.S: Characters and Diversification Rates (Summary)
  95. 13.01: The Evolution of Self-Incompatibility
  96. 13.02: A State-Dependent Model of Diversification
  97. 13.03: Calculating Likelihoods for State-Dependent Diversification Models
  98. 13.04: ML and Bayesian Tests for State-Dependent Diversification
  99. 13.05: Potential Pitfalls and How to Avoid Them
  100. 14: What have we learned from the trees
  101. 14.0S: 14.S: What have we learned from the trees? (Summary)
  102. 14.01: The Lorax
  103. 14.02: What We Have Learned so Far
  104. 14.03: Where Can we go Next?
  105. 14.04: A hint at the future of comparative methods