This page contains data files, corrections, & other supplementary information for the book entitled Phylogenetic Comparative Methods in R by Liam Revell & Luke Harmon (2022; Princeton University Press).

For all other information, including how to purchase the book (which we recommend considering), please refer to the Princeton University Press page for the book: https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r.

Corrections, data files, and other supplementary information

Chapter 1: A brief introduction to phylogenetics in R

Corrections to Chapter 1.
Supplement to Chapter 1.

  1. anole.data.csv: Log-transformed continuous trait data for 100 Caribbean Anolis lizards in CSV format. Source: Mahler et al. (2010).
  2. Anolis.tre: Time-calibrated phylogenetic tree with 100 Caribbean Anolis lizard species in simple Newick format. Source: Mahler et al (2010).
  3. ecomorph.csv: Discrete ‘ecomorphological category’ data for 82 Caribbean Anolis lizard species in CSV format. Source: Mahler et al. (2010).
  4. phel.csv: Phenotypic trait data for Phelsuma geckos in CSV format. Source: Harmon et al. (2010).
  5. phel.phy: Phylogenetic tree for Phelsuma in simple Newick format. Source: Harmon et al. (2010).

Chapter 2: Phylogenetically independent contrasts

  1. Barbetdata.csv: Trait data Asian barbets (Megalaimidae) in CSV format. Source: Gonzalez-Voyer et al. (2013).
  2. BarbetTree.nex: Phylogenetic tree of Asian barbets (Megalaimidae) in NEXUS format. Source: Gonzalez-Voyer et al. (2013).
  3. mammalHR.csv: Trait data for body mass (in kg) and home range size (in km2) for 49 species of mammals. Source: Garland et al. (1992).
  4. mammalHR.phy: Phylogenetic tree of mammals. Source: Garland et al. (1992).

Chapter 3: Phylogenetic generalized least squares

Corrections to Chapter 3.
Supplement to Chapter 3.

  1. anole.data.csv: Log-transformed continuous trait data for 100 Caribbean Anolis lizards in CSV format. Source: Mahler et al. (2010).
  2. Anolis.tre: Time-calibrated phylogenetic tree with 100 Caribbean Anolis lizard species in simple Newick format. Source: Mahler et al (2010).
  3. Barbetdata.csv: Trait data Asian barbets (Megalaimidae) in CSV format. Source: Gonzalez-Voyer et al. (2013).
  4. BarbetTree.nex: Phylogenetic tree of Asian barbets (Megalaimidae) in NEXUS format. Source: Gonzalez-Voyer et al. (2013).
  5. ecomorph.csv: Discrete ‘ecomorphological category’ data for 82 Caribbean Anolis lizard species in CSV format. Source: Mahler et al. (2010).
  6. primateEyes.csv: Phenotypic data for primate skull size, orbital area, and diel activity pattern in CSV format. Source: Kirk and Kay (2004). (See corrections.)
  7. primateEyes.phy: Phylogeny of primates. Source: Kirk and Kay (2004).

Chapter 4: Modeling continuous character evolution on a phylogeny

Corrections to Chapter 4.

  1. bac_rates.csv: Phenotypic trait data for genome size and mutation rate across 34 different bacterial species in CSV format. Source: Gibson and Eyre-Walker (2019).
  2. bac_rates.phy: Phylogenetic tree for 34 bacterial species in simple Newick format. Source: Gibson and Eyre-Walker (2019).

Chapter 5: Multi-rate, multi-regime, and multivariate models for continuous traits

  1. anole.data.csv: Log-transformed continuous trait data for 100 Caribbean Anolis lizards in CSV format. Source: Mahler et al. (2010).
  2. anolis.mapped.nex: Phylogenetic tree of Anolis in NEXUS format with ecomorphological category mapped onto the nodes and edges. Source: Mahler et al. (2010); this book.
  3. Centrarchidae.csv: Trait data for 28 centrarchid fish species. Source: Revell and Collar (2008).
  4. Centrarchidae.nex: Phylogenetic tree of centrarchid fish species in NEXUS format with feeding mode mapped onto the nodes and edges of the tree. Source: Revell and Collar (2008); this book.
  5. cordylid-data.csv: Trait data from a phylogenetic PCA of morphological trait data in lizards of the family Cordylidae in CSV format. Source: Broeckhoven et al. (2016).
  6. cordylid-tree.phy: Phylogenetic tree of lizards of the family Cordylidae in simple Newick format. Source: Broeckhoven et al. (2016).
  7. ecomorph.csv: Discrete ‘ecomorphological category’ data for 82 Caribbean Anolis lizard species in CSV format. Source: Mahler et al. (2010).
  8. Iguania.csv: Continuous phenotypic trait data for 282 iguanian lizard species in CSV format. Source: Harmon et al. (2010).
  9. Liolaemidae.phy: Phylogenetic tree of liolaemid lizards in simple Newick format. Source: Harmon et al. (2010).
  10. mammalHR.csv: Trait data for body mass (in kg) and home range size (in km2) for 49 species of mammals. Source: Garland et al. (1992).
  11. mammalHR.phy: Phylogenetic tree of mammals. Source: Garland et al. (1992).
  12. Phrynosomatidae.phy: Phylogenetic tree of phrynosomatid lizards in simple Newick format. Source: Harmon et al. (2010).

Chapter 6: Modeling discrete character evolution on a phylogeny

Corrections to Chapter 6.

  1. squamate.tre: Phylogenetic tree of squamates in NEXUS format. Source: Brandley et al. (2008).
  2. squamate-data.csv: Data set of hindfoot digit number for 120 species of squamates. Source: Brandley et al. (2008); this book.

Chapter 7: Other models of discrete character evolution

Supplement to Chapter 7.

  1. anolis.mapped.nex: Phylogenetic tree of Anolis in NEXUS format with ecomorphological category mapped onto the nodes and edges. Source: Mahler et al. (2010); this book.
  2. bonyfish.csv: Phenotypic trait dataset for parental care and spawning mode of bony fish in CSV format. Source: Benun Sutton and Wilson (2019).
  3. bonyfish.tre: Phylogenetic tree of bony fish in simple Newick format. Source: Benun Sutton and Wilson (2019).
  4. dewlap.colors.csv: Phenotypic trait dataset for dominant dewlap color and other traits in Anolis lizards in CSV format. Source: Ingram et al. (2016).
  5. Liolaemidae.data.csv: Phenotypic trait data for parity mode, maximum altitude, and environmental temperature in lizards of the family Liolaemidae in CSV format. Source: Esquerre et al. (2019)
  6. Liolaemidae.MCC.nex: Phylogenetic tree of lizards in the family Liolaemidae. Source: Esquerre et al. (2019).
  7. lizard_spines.csv: Habitat and tail spine data for 658 species of lizards, in CSV format. Source: Ramm et al. (2019).
  8. lizard_tree.nex: Phylogenetic tree of lizards, in NEXUS format. Source: Ramm et al. (2019).
  9. Mycalesina_habitat.csv: Habitat data for butterflies from the subtribe Mycalesina. Source: Halali et al. (2020).
  10. Mycalesina_phylogeny.nex: Phylogenetic tree of butterflies of the subtree Mycalesina. Source: Halali et al. (2020).
  11. planaria.csv: Habitat data for 28 species of flatworms. Source: Benitez-Alvarez et al. (2020).
  12. planaria.timetree.nex: Ultrametric tree of 28 flatworm species. Source: Benitez-Alvarez et al. (2020); this book.
  13. pollen-data.csv: Data for pollen grain type for in flowering plants in CSV format. Source: Williams et al. (2014).
  14. pollen-tree.phy: Phylogenetic tree of 511 plant species in simple Newick format. Source: Williams et al. (2014).
  15. squamate.tre: Phylogenetic tree of squamates in NEXUS format. Source: Brandley et al. (2008).
  16. squamate-data.csv: Data set of hindfoot digit number for 120 species of squamates. Source: Brandley et al. (2008); this book.

Chapter 8: Reconstructing ancestral states

Supplement to Chapter 8.

  1. anole.data.csv: Log-transformed continuous trait data for 100 Caribbean Anolis lizards in CSV format. Source: Mahler et al. (2010).
  2. Anolis.tre: Time-calibrated phylogenetic tree with 100 Caribbean Anolis lizard species in simple Newick format. Source: Mahler et al (2010).
  3. elopomorph.csv: Phenotypic data for feeding mode and total length for 61 eel species. Source: Collar et al. (2014).
  4. elopomorph.tre: Phylogenetic tree of eels in simple Newick format. Source: Collar et al. (2014).

Chapter 9: Analysis of diversification with phylogenies

  1. 10kTrees_Primates.nex: File with 100 phylogenetic trees of primates in NEXUS format. Source: https://10ktrees.nunn-lab.org/.
  2. etheostoma_percina_chrono.tre: Time-calibrated phylogenetic tree of 201 species of darter fishes in simple Newick format. Source: Near et al. (2011).

Chapter 10: Time and density dependent diversification

  1. Anolis.tre: Time-calibrated phylogenetic tree with 100 Caribbean Anolis lizard species in simple Newick format. Source: Mahler et al (2010).
  2. Cetacea.phy: Phylogenetic tree of whales and dolphins in simple Newick format. Source: Morlon et al. (2011).

Chapter 11: Character-dependent diversification

  1. Anolis.tre: Time-calibrated phylogenetic tree with 100 Caribbean Anolis lizard species in simple Newick format. Source: Mahler et al (2010).
  2. Coccoidea_hosts.csv: Data file containing number of host families for different species of scale insects in CSV format. Source: Hardy et al. (2016).
  3. Coccoidea_phylogeny.tre: Phylogenetic tree of scale insects in simple Newick format. Source: Hardy et al. (2016).
  4. grunts.csv: Trait data for different fish species in the family Haemulidae in CSV format: Source: Price et al. (2013).
  5. grunts.phy: Phylogenetic tree of haemulid fishes in simple Newick format. Source: Price et al. (2013).
  6. pipefishes.phy: A phylogenetic tree for Syngnathidae. Source: Hamilton et al. (2017).
  7. squamate.tre: Phylogenetic tree of squamates in NEXUS format. Source: Brandley et al. (2008).
  8. squamate-data.csv: Data set of hindfoot digit number for 120 species of squamates. Source: Brandley et al. (2008); this book.
  9. terapontidae.csv: Phenotypic trait data for fishes of the family Terapontidae in CSV format. Source: Davis et al. (2016).
  10. terapontidae.phy: Phylogenetic tree for terapontid fishes in simple Newick format. Source: Davis et al. (2016).

Chapter 12: Biogeography and community ecology

  1. attine-distribution-data.txt: Geographic distribution data for Attini ants in modified PHYLIP format. Source: Bransetter et al. (2017).
  2. attine-tree-pruned.tre: Phylogenetic tree for ants in the tribe Attini in simple Newick format. Soruce: Bransetter et al. (2017).
  3. SJ_ComMatrix.csv: Presence/absence data for plant species in 80 sites across the San Juan Islands in CSV format. Source: Marx et al. (2016).
  4. SJtree.phy: Phylogenetic tree of the regional species pool for plant species of the San Juan Islands in simple Newick format. Source: Marx et al. (2016).

Chapter 13: Plotting phylogenies and comparative data

Corrections to Chapter 13.

  1. attine-tree-pruned.tre: Phylogenetic tree for ants in the tribe Attini in simple Newick format. Soruce: Bransetter et al. (2017).
  2. vert-data.csv: Data for mass, length, and clutch/litter size in 11 species of vertebrates. Source: this book.