Lecture Notes

Lecture notes and other course materials will be posted here in reverse chronological order

Lecture 23 - Thursday, Nov. 19, 2009

• Spatial genetic autocorrelation. Notes Slides

Lecture 22 - Tuesday, Nov. 17, 2009

• Mantel Test 2. Partial Mantel Tests. Notes (no slides)
• Reminder: Homework Assignment 4 due today by 5 pm.

Lecture 21 - Thursday, Nov. 12, 2009

• Isolation by distance. Mantel Test I. Notes Slides
• Reminder: Homework Assignment 4 due Tuesday by 5 pm.

Lecture 20 - Tuesday, Nov. 10, 2009

Lecture 19 - Thursday, Nov. 5, 2009

• Differentiation and migration of nuclear vs. biparentally inherited genomes. Notes Slides

Lecture 18 - Tuesday, Nov. 3, 2009

• Discussion of O'Reilly et al. (2004). Notes (no slides)

Lecture 17 - Thursday, Oct. 29, 2009

• Migration Models I. Microsatellite evolution and homoplasy. Notes Slides
• Reminder
• Read O'Reilly et al. (2004) for discussion in class on Tuesday:
• O'Reilly, P. T., M. F. Canino, K. M. Bailey, and P. Bentzen. 2004. Inverse relationship between F-ST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology 13:1799–1814.

Lecture 16 - Tuesday, Oct. 27, 2009

• Genetic distances, distance matrix methods, and population trees. Notes Slides
• Tree-Thinking Exercise. Download
• Complete this self-assessment prior to discussion in class on Thursday.

Lecture 15 - Thursday, Oct. 22, 2009

• Discussion of Garroway et al. (2008). Population Graphs finalé. Slides (no notes)

Lecture 14 - Tuesday, Oct. 20, 2009

• Population Graphs. Notes Slides
• Reminder
• Read Garroway et al. (2008) for discussion in class on Thursday:
• Garroway, C. J., J. Bowman, D. Carr, and P. J. Wilson. 2008. Applications of graph theory to landscape genetics. Evolutionary Applications 1:620-630.

Lecture 13 - Thursday, Oct. 15, 2009

• Euclidean distances and genetic coding in AMOVA. Notes Slides

Lecture 12 - Tuesday, Oct. 13, 2009

• AMOVA and permutation tests of significance. Slides (no Notes)
• Reminder: Grading of Problem Set 3 to be completed today.

Lecture 11 - Thursday, Oct. 7, 2009

• Calculating F-statistics over multiple alleles and loci. Notes Slides
• Note: We spent most of this lecture discussion Holsinger and Weir (2009).
• Reminder: Grading of Problem Set 3 to be completed Tuesday by the beginning of class.

Lecture 10 - Tuesday, Oct. 5, 2009

• Estimation of F-statistics via ANOVA. Notes Slides
• Reminders: 
• Problem Set 3 due today.
• Key to Problem Set 3. Download
• Reading for discussion in class on Thursday:
• Holsinger, K. E., and B. S. Weir. 2009. Genetics in geographically structured populations: defining, estimating and interpreting F_ST. Nature Reviews Genetics 10:539-650.

Lecture 9 - Thursday, Oct. 1, 2009

• A bit more on F-statistics. Notes Slides
• Example data set used in class to demonstrate the estimation of Wright's F-statistics using the program GDA. Download
• Reminder: Problem Set 3 due Tuesday, Oct. 6, by the beginning of class.

Lecture 8 - Tuesday, Sept. 29, 2009

• Wright's F-statistics as measures of identity by descent. Notes Slides
• Scan of Hartl & Clark pp.114-118 re F-statistics for 3-level hierarchical models. Download
• Grading of Problem Set 2 to be completed today by beginning of class.
• Problem Set 3 posted today.
• Due Tuesday, Oct. 6, by the beginning of class.
• This problem set must be completed using Google Documents, in particular the Google Docs Spreadsheet, as explained for Problem Set 2 (see instructions under Lecture 5).
• Problem Set 3. Download
• Data sets for use with Problem Set 3. Download Zip Archive

Lecture 7 - Thursday, Sept. 24, 2009

• Wright's F-statistics. Notes (no slides)
• Handout re calculation of Wright's F-statistics. Download

Lecture 6 - Tuesday, Sept. 22, 2009

• Derivation of population-level F. Inbreeding depression and its effects. Notes Slides
• Problem Set 2 due today at the beginning of class. 
• Problem Set 2 Key. Download
• Student grading of Problem Set 2 must be completed by Tuesday, Sept. 29.

Reminder - No lecture Thurs.-Thurs., Sept. 10-17

Lecture 5 - Tuesday, Sept. 8, 2009

• Individual- and population-level inbreeding (plus in-class exercises). Notes Slides
• Problem Set 1 due today at the beginning of class. 
• Problem Set 1 Key. Download
• Problem Set 2 posted today.
• Due Tuesday, Sept. 22, by the beginning of class.
• This problem set must be completed using Google Documents, in particular the Google Docs Spreadsheet.
• Problem Set 2. Download
• Instructions for completing and sharing this assignment using Google Documents. Download

Lecture 4 - Thursday, Sept. 3, 2009

• Testing HWE. Intro to assortative mating and inbreeding. Download Notes Slides
• Data for in class test of HWE using GenAlEx. Download
• Data for in class test of HWE using GenePop. Link 
• Reminder
• Problem Set 1 due Tuesday, Sept. 8, by the beginning of class.

Lecture 3 - Tuesday, Sept. 1, 2009

• Derivation of and testing for Hardy-Weinberg equilibrium. Download Notes Slides
• In-class exercise. Download
• Problem Set 1. Download
• Due next Tuesday, Sept. 8, by the beginning of class.

Lecture 2 - Thursday, Aug. 27, 2009

• Notation and introduction to the Hardy-Weinberg Principle. Download Notes Slides
• In-class exercise. Download
• Handout re standard genotype and allele notation and calculations. Download

Lecture 1 - Tuesday, Aug. 25, 2009

• The nature and organization of genetic variation. Download Notes