Main hub. I suggest setting a bookmark to this page.      RELOAD/REFRESH FROM TIME TO TIME!!
Underlined text is generally hot-linked (mostly blue; some blue text in internal pages is not underlined and not hotlinked)

Glossary of terms used in Population Genetics  

  Download "WebSoftware.doc" list of software resources for pop. gen. and some phlogenetics

Go to web page outlining major aspects of analyzing genetic population structure (WAAP.html)
   (some important measures to calculate, very basic intro. to the practicalities of running a few of the many software choices)

     Jump to navigation help note

            Jump to reading list, syllabus and course calendar                       Go to Dave McDonald's home page

Lecture Notes

Go to Lecture 1      (Tu 29-Aug-06)    [Intro. to course -- topics covered, essentials of DNA as a genetic marker]
Go to Lecture 2     (Th 31-Aug-06)                 [Overview of phylogenetics]
Go to Lecture 2a   (Th 31-Aug & Tu 5-Sep)   [Speciation and hybridization]
Go to Practicum # 1   (Th 7-Sep)             -- tree-building with PHYLIP

Go to Lecture 3     (Th 13-Sep)       [Population Genetics I -- Intro., Hardy-Weinberg]
Go to Lecture 4     (Th 13-Sep)       [Population Genetics II -- Heterozygosity, H_E or D; intro. to F_ST]
Go to Lecture 5     (Tu 19-Sep)       [Population Genetics III -- Wahlund effect, isolate breaking, PHSC approach to F_ST]
Go to Lecture 6     (Tu 25-Sep)       [Population Genetics IV -- Genetic distances: Cavalli-Sforza chord, Nei's, Reynolds']
Go to Lecture 7     (Tu 10-Oct)        [Population Genetics V -- N_e, effective population size; overview of alternative markers]
Go to Lecture 8     (Tu 18-Oct)        [Population Genetics VI -- intro. to microsatellites as a genetic marker]
Go to Lecture 9                               [Population Genetics VII -- ]
Go to Lecture 11    (Tu 14-Nov)      [Conservation genetics]

Lecture notes beyond this point have not yet been revised for 2006 

Go to Lecture 12                             [Highlights of the course]

Lecture notes are under construction (and some links may not yet work). Beyond the red text are lectures from previous years, subject to extensive revision, and placed here in case you want to get a feel for future topics.

Homework pages

Download Word document  PHYLIPinfo.doc      

Download Excel sheet of worked example of UPGMA, Neighbor-joining and Fitch-Margoliash tree from great ape 5-taxon distance matrix

Download Word doc. of steps for UPGMA & NJ            

For full list of references (~ 1,400 references, many with abstracts), e-mail me and I will send you a Word attachment or transfer it to a Zip disk or diskette.

Go to Syllabus (excluding calendar page and reading list)       Go to course calendar (Calendar.html)

        Download "WebSoftware.doc" list of software resources

        Glossary of terms used for Genetic/Molecular Markers

 Download Excel spreadsheet guide (Hexp.XL) to calculating expected heterozygosity, H_exp (or as Bruce Weir prefers to call it, Gene Diversity, D)       

Go to web page describing how to calculate F_ST from heterozygosities (FST.html).   

Download Excel spreadsheet HominTrees.XL demo. of construction of UPGMA , Fitch-Margoliash and neighbor-joining trees.

Dr. David McDonald    BioSciences 413       dbmcd@uwyo.edu     766-3012
Office hours W, Th 10:00-12:00 or by appointment

A note on navigating the web pages:
Figures, Equations and Required Readings are labeled in a "chapter-like" manner, with each lecture as the equivalent of a chapter.  That is, Lecture 1's web page will be "Chapter 1".  All Figures in that web page will be numbered Fig. 1.1, 1.2, ...1.n for the n Figures it includes.  The same will be true for Equations (numbers for which will be toward the right-hand margin).  I will try to hotlink most references to Figures or Equations WITHIN a web page, but may not do so BETWEEN web pages.  That is, a reference to Eqn 1.1 in the 2nd web page ("Chapter 2") might require you to jot that number down and surf back later.  The hotlinks will be the standard underline format.  I will have links between all the web pages that I design for this course.  I may even put in some external links. Come see me if you need help on browsing the web pages.  Please let us know, also, if you find typos, pages that won't print properly, or other glitches.
Reading numbers may change if the lecture schedule shifts -- the updated list of number will be reposted occasionally both on the web and in the Science Library Reserve Folder.