Analysis of Phylogenetics and Evolution with R

Second Edition — 2012

The page on Springer's Web site is HERE.

An animated version of Fig. 3.2. The original PDB file: bdna.pdb.

• The solutions of the exercices (work in progress)
• A gzipped archive with the data files and the R scripts: APER2_Online_Material.tar.gz [800 KB].
  You can download the individual files below:
  • The data files:
    • host_parasite.tre The host–parasite (Chaetodipus–Fahrenholzia) trees used to make Fig. 4.21.
    • mammal_mtGenome.fasta [3.9 MB] The 233 mammalian mitochondrial genomes used as a case study in Chapter 3.
    • primfive.tre The five primate species tree used in many examples in Chapter 6.
    • rodent_clock.tre The ultrametric tree of 14 species of rodents used for Fig. 4.20.
    • rodent.tre The tree of 14 species of rodents used in several examples in Chapter 4.
    • sylvia_data.txt The ecological data of the Sylvia warblers for the case studies in Chapters 3, 5, and 6.
    • sylvia.txt The sequence data for the Sylvia warblers.
  • The scripts of R commands used in the case studies:
    • SylviaWarblers.R
    • MammalianMitochondrialGenomes.R
    • ButterflyDNABarcodes.R
• The list of errata.
• Some additional figures and videos:

This a colour version of Fig. 3.7. Actually, AAstat does not allow the user to modify the colours, and I modified it to make the BW version in the book.

An example of the use of image with DNA sequences showing the default colours (which can be modified, see below).

A variation around Fig. 3.8: the differences are the colour (blue instead of black) and the grid which, instead of marking each column as in the book, shows blocks of three columns (thus, 51 columns are displayed instead of 50 in the book). The code is: image(woodmouse[, 1:51], c("g", "n"), c("blue", "grey")) grid(51/3, 15, col = "black")

Another version of Fig. 5.11 showing the idea behind consensus networks. The shades of grey have been replaced by colours.

Figure 5.16 with the colours used by default by lattice.

Figure 7.4 with the colours used by default by diversitree—looking nicer than the shades of grey.

First Edition — 2006

The page of this book on Springer's Web site is HERE.

You can find here:

• The data files and script files (as a zipped tar archive) to repeat the analyses in the "Case Studies" (this includes the two rodent trees forgotten in the same file on Springer's site).
• The list of errata.
• A list of updates pointing to the new features accomplished since the text of the book was completed (February 2006).
• The solutions to the exercices.

• Daniel Stoebel. 2007. Quarterly Review of Biology 82: 148. DOI: 10.1086/519586
• Barbara R. Holland. 2007. Systematic Biology 56: 694–696. DOI: 10.1080/10635150701475589
• Marc A. Suchard. 2007. Biometrics 82: 1304–1305. DOI: 10.1111/j.1541-0420.2007.00905_11.x
• M. Last. 2007. Journal of the American Statistical Association 102: 1477–1478. DOI: 10.1198/jasa.2007.s239
• Vincent Careau. 2007. Écoscience 14: 399–400. URL: https://www.jstor.org/stable/42902051