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Intro Materials

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Jamie R. Oaks edited this page Oct 1, 2025 · 1 revision

Below are some resources for getting more familiar with some of the concepts and skills relevant to our lab group. You can find some of the resources mentioned below in the "literature" directory of our lab's shared Box folder.

Population genetics

  • I (Jamie) like John Gillespie's book "Population Genetics: A Concise Guide". I don't have a PDF of this book and it's a bit old. If I were a student now, I would probably opt for Graham Coop's free online pop gen textbook: https://github.com/cooplab/popgen-notes (if you scroll down, there's a link to the PDF). I haven't read Coop's book, but I suspect it's good and a more modern substitute for Gillespie's book
  • I recommend Dick Hudson's 1990 chapter on the coalescent (you can find it in the lab Box folder)
  • Ziheng Yang gives a nice intro the the coalescent in Chapter 9 of his book, Molecular Evolution: A Statistical Approach. (you cna find this in the lab Box folder).

Phylogenetics

Book chapter by Paul Lewis on likelihood-based phylogenetics:

  • Find Lewis-1999-molecular-systematics-of-plants.pdf in the lab's "literature" Box directory

Phylogenetics 101 videos by Paul Lewis:

Lots of great recorded talks on phyloseminar.org

Ziheng Yang's Molecular Evolution book (see the lab Box folder). Probably best used as a reference for specific topics.

Luke Harmon's free book, Phylogenetic Comparative Methods: Learning from trees

Brian O'Meara's open graduate course on phylogenetics methods, Phylometh

Math primers for the theory side of phylogenetics and evolution

Fantastic video series by 3Blue1Brown (Grant Sanderson). All of his videos are on YouTube, but I prefer to access them through the 3blue1brown website because I find it better organized and there are tutorials below some of the videos. If you go to his site and scroll down to the topics you can find the video series below (but I can't link directly to them, so below I'm linking to the YouTube playlists, but again I think going to his website provides a better experience).

Sally Otto's book A Biologist's Guide to Mathematical Modeling in Ecology and Evolution (See lab Box folder)

Computational basics

Command line basics

Software Carpenty's Unix Shell lesson:

My attempt at teaching this:

Version control with Git

Software Carpenty's Git lesson:

My attempt at teaching this:

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