I developed this book as a collection of the concepts, methods, and applications that I most wanted to share with students in my Phylogenetic Biology courses. It is really my lecture notes dressed up in the form of the rough draft of a book.
0.1 Additional resources
Please see the appendices for a variety of additional resources.
Thanks in particular to the students of Yale EEB354 in the fall of 2020. This book started as a collection of lecture notes for this course, the first that I taught fully online. The students provided invaluable motivation, feedback, and patience. Thanks in particular to Lauren Mellenthin, the graduate teaching fellow for the course, for her incredible contributions to this course and, as a result, this book. Members of my lab provided very helpful feedback when I posted new chapters. Steve Haddock and Felipe Zapata provided close reads of host chapters, often within hours of completing first drafts.
This book is dedicated to my sister Jenny Dunn, who has been there every step of the way. I am so grateful for her adventurous spirit, quick mind, and shared love of life. Thank you Jenny.
0.4 Source code
Please submit any errors you find, typos, or suggestions that you have for improving the manuscript to the issue tracker.
0.5 Other resources
The following sites have a wide variety of material that is relevant to the theory and and practice of phylogenetic biology.
An extensive list of tools, tutorials, and examples of phylogenetic tools in the programming language R maintained by Briam O’Meara: CRAN Task View: Phylogenetics
The Workshop on Molecular Evolution at Woods Hole. This is an intensive summer course on phylogenetics, with an emphasis on building phylogenetic trees. Check out the faculty pages for lecture pdfs: Workshop on Molecular Evolution
The Applied Phylogenetics Workshop in Bodega Bay. This is another summer course on phylogenetics, but with a bit more emphasis on using phylogenies to test evolutionary questions: Applied Phylogenetics Workshop
The following books are great resources for learning more about phylogenetic biology:
Baum, D. and Smith, S. (2012). Tree Thinking. An Introduction to Phylogenetic Biology. Roberts Publishers.
Paradis, E. (2011) Analysis of Phylogenetics and Evolution with R. Springer
Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates.
Swofford, D. L., Olsen, G. J., Waddell, P. J., & Hillis, D. M. (1996). Phylogenetic inference. In: Molecular Systematics, Second Edition. eds: D. M. Hillis, C Moritz, & B. K. Mable. Sinauer Associates
The following books provide general computational background for the topics covered here:
0.6 Software versions
This book was rendered from the source code on \(Thu Nov 05 10:57:12 PM 2020\) with the following R package versions.
R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.1 LTS Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  kableExtra_1.3.1 phangorn_2.5.5 Matrix_1.2-18 forcats_0.5.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0  tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0 stringr_1.4.0 phytools_0.7-70 maps_3.3.0  magrittr_1.5 gridExtra_2.3 geiger_2.0.7 ape_5.4-1 ggtree_2.4.0 treeio_1.14.0 loaded via a namespace (and not attached):  subplex_1.6 nlme_3.1-149 fs_1.5.0 lubridate_1.7.9 webshot_0.5.2  httr_1.4.2 numDeriv_2016.8-1.1 tools_4.0.3 backports_1.2.0 R6_2.5.0  DBI_1.1.0 lazyeval_0.2.2 colorspace_1.4-1 withr_2.3.0 tidyselect_1.1.0  mnormt_2.0.2 compiler_4.0.3 cli_2.1.0 rvest_0.3.6 expm_0.999-5  xml2_1.3.2 bookdown_0.21 scales_1.1.1 mvtnorm_1.1-1 quadprog_1.5-8  digest_0.6.27 rmarkdown_2.5 pkgconfig_2.0.3 htmltools_0.5.0 plotrix_3.7-8  highr_0.8 dbplyr_1.4.4 rlang_0.4.8 readxl_1.3.1 rstudioapi_0.11  generics_0.1.0 combinat_0.0-8 jsonlite_1.7.1 gtools_3.8.2 patchwork_1.0.1  fansi_0.4.1 Rcpp_1.0.5 munsell_0.5.0 lifecycle_0.2.0 scatterplot3d_0.3-41  stringi_1.5.3 yaml_2.2.1 clusterGeneration_1.3.5 MASS_7.3-53 grid_4.0.3  blob_1.2.1 parallel_4.0.3 crayon_1.3.4 lattice_0.20-41 haven_2.3.1  hms_0.5.3 tmvnsim_1.0-2 knitr_1.30 pillar_1.4.6 igraph_1.2.6  fastmatch_1.1-0 reprex_0.3.0 glue_1.4.2 evaluate_0.14 BiocManager_1.30.10  modelr_0.1.8 deSolve_1.28 vctrs_0.3.4 cellranger_1.1.0 gtable_0.3.0  assertthat_0.2.1 xfun_0.19 broom_0.7.2 tidytree_0.3.3 coda_0.19-4  viridisLite_0.3.0 aplot_0.0.6 rvcheck_0.1.8 ellipsis_0.3.1
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Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://github.com/rstudio/bookdown.