Human Evolutionary Genetics

Introduction

This repository contains materials for a course I taught from 2000 through 2024 under the title Human Evolutionary Genetics. I taught it first on my own, then with Henry Harpending, and then (for years and years) with Jon Seger. During the final semester, Jon and I taught it together with Angela Hancock. It was cross-listed at the University of Utah between the Anthropology and Biology Departments under the designations Anth5221 and Biol5221.

The files on the website for this course are of several types: lecture slides, tutorials, and so on. Most of these are written in LaTeX or Markdown, and the sources are in various subdirectories.

For this public github repository, I've removed all copyrighted files. Consequently, the .html and .php files have some dead links to these missing files.

The website from the most recent version of the course can be found here.

The contents of the top-level directory in this github repository are as follows:

• homework contains a 43-page collection of algebraic homework exercises, with answers to even-numbered exercises at the back.

• lab contains a 59-page lab manual

• slides contains lecture slides

• tutorial contains tutorials on a variety of subjects

• exam contains source code for 3 exams

• src contains Python source code for all the lab assignments

• syllabus contains the main course syllabus

• labsyl contains the lab syllabus

• studyguide contains some outdated study guides. I stopped updating these a few years ago, because the homework, lecture slides, and lab materials are better sources than the study guides ever were.

• txt contains a 74-page introduction to gene genealogies, also known as "coalescent theory".

• websrc contains Markdown code, which creates HTML or PHP files, which provide much of the structure of the website.

• website contains the entire website. When I update any of the files mentioned above, the next step is to copy it into the appropriate position with the website subdirectory.

• Makefile is described below.

Pushing files onto a remote web server

On my websites, I use PHP code to display the time at which each file was last modified. This enables students to tell whether they are looking at a new version the file, or one from some previous semester. Unfortunately, github doesn't allow PHP on pages it hosts, so I don't use its hosting service. The following paragraphs describe the method I use for pushing files from the website directory below onto a web server at the University of Utah.

On my personal computer, there is a directory for each course, and each of these has a subdirectory called website. When I modify a file, the next step is to copy the file (sometimes changing its name) into the appropriate place within the website subdirectory for the course.

There is also a global website directory immediately below the home directory on my personal computer. This is a mirror image of my website on the remote server. It contains (among other things) a subdirectory for each course. When I've made changes to the website subdirectory of a course, the next step is to push them into this global website directory. To do this, cd into the top-level directory of the course and type make website. This calls the make command, which reads the file Makefile in the current directory and then copies the course website tree into the global website.

The final step is to push the global website onto the remote server. The details of this step will depend on the hosting service you use, so all I can do is describe how it works in my own computing environment. I use a shell script whose contents are shown below. It uses the rsync command to copy an entire directory tree from one place to another. The --delete option deletes remote files that are not in the local website directory. This means that you can delete files from the server simply by removing them from the local directory.

If your hosting service allows you to use the rsync command directly, then add -e ssh to the rsync command below. This compresses and encrypts the content and makes things much faster. My university's hosting service no longer supports this. One must instead mount the remote directory using SMB (Windows) or SAMBA (Linux or Mac). In this setup, -e ssh would not save time or improve security, because the compression and decompression steps would both happen on the local machine. In this new setup, the process of pushing to the server is much slower.

The shell script below should be copied into a file within your own $HOME/bin directory and marked as executable. You'll need to modify the rsync command so that it specifies a destination on your own web hosting service.

#!/bin/sh

# Remove backup files made by the text editor
find ~/website -name "*~" -exec rm {} \;

# Make everything readable by everyone
chmod -R go+r ~/website/*

# Make directories executable
find ~/website -type d -exec chmod +x {} \;

# Copy the directory tree below $HOME/website onto the remote
# server, which is mounted using SMB/SAMBA.
cd; rsync -rptvz --copy-links --delete website/    \
  /Volumes/u0028949/html-docs/public_html/

On my machine, this executable shell script is called installcsbs. After mounting the remote directory using SAMBA, I type installcsbs to copy the website directory from my local machine onto the remote server.