Preface

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.

0.2 Acknowledgements

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.

0.3 Dedication

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

The source code for this manuscript is available on github. The book was rendered from the source with bookdown (Xie 2016).

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 \(Sun Oct 25 09:47:18 2020\) with the following R package versions.

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] kableExtra_1.2.1 phangorn_2.5.5   Matrix_1.2-18    forcats_0.5.0   
 [5] dplyr_1.0.2      purrr_0.3.4      readr_1.3.1      tidyr_1.1.2     
 [9] tibble_3.0.3     ggplot2_3.3.2    tidyverse_1.3.0  stringr_1.4.0   
[13] phytools_0.7-47  maps_3.3.0       magrittr_1.5     gridExtra_2.3   
[17] geiger_2.0.7     ape_5.4-1        ggtree_2.2.4     treeio_1.12.0   

loaded via a namespace (and not attached):
 [1] subplex_1.6             nlme_3.1-149            fs_1.5.0               
 [4] lubridate_1.7.9         webshot_0.5.2           httr_1.4.2             
 [7] numDeriv_2016.8-1.1     tools_4.0.2             backports_1.1.10       
[10] R6_2.4.1                DBI_1.1.0               lazyeval_0.2.2         
[13] colorspace_1.4-1        withr_2.2.0             tidyselect_1.1.0       
[16] mnormt_2.0.2            compiler_4.0.2          cli_2.0.2              
[19] rvest_0.3.6             animation_2.6           expm_0.999-5           
[22] xml2_1.3.2              bookdown_0.20           scales_1.1.1           
[25] mvtnorm_1.1-1           quadprog_1.5-8          digest_0.6.25          
[28] rmarkdown_2.3           pkgconfig_2.0.3         htmltools_0.5.0        
[31] plotrix_3.7-8           dbplyr_1.4.4            rlang_0.4.7            
[34] readxl_1.3.1            rstudioapi_0.11         generics_0.0.2         
[37] combinat_0.0-8          jsonlite_1.7.1          gtools_3.8.2           
[40] patchwork_1.0.1         fansi_0.4.1             Rcpp_1.0.5             
[43] munsell_0.5.0           lifecycle_0.2.0         scatterplot3d_0.3-41   
[46] stringi_1.5.3           yaml_2.2.1              clusterGeneration_1.3.4
[49] MASS_7.3-53             grid_4.0.2              blob_1.2.1             
[52] parallel_4.0.2          crayon_1.3.4            lattice_0.20-41        
[55] haven_2.3.1             hms_0.5.3               tmvnsim_1.0-2          
[58] knitr_1.29              pillar_1.4.6            igraph_1.2.5           
[61] fastmatch_1.1-0         reprex_0.3.0            glue_1.4.2             
[64] evaluate_0.14           BiocManager_1.30.10     modelr_0.1.8           
[67] deSolve_1.28            vctrs_0.3.4             cellranger_1.1.0       
[70] gtable_0.3.0            assertthat_0.2.1        xfun_0.17              
[73] broom_0.7.0             tidytree_0.3.3          coda_0.19-3            
[76] viridisLite_0.3.0       aplot_0.0.6             rvcheck_0.1.8          
[79] ellipsis_0.3.1         

0.7 License

This manuscript is distrubuted under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License.

References

Xie, Yihui. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://github.com/rstudio/bookdown.