Biol 5221: Lectures and Reading Assignments

In the list below, the numbers indicate lecture topics. Click on one, and you'll get the slides we showed in class. Lectures are assigned on dates listed in the syllabus. More than one lecture may be assigned on a given date. The dates in the list below tell you when the lecture slides were added to this website. Under each lecture topic, the open circles indicate additional readings. Some of these are clickable too and take you to the reading itself, in pdf format. You'll need a pdf reader such as Adobe Acrobat Reader or xpdf. If the reading is under copyright, you'll be asked for a username and password. If you didn't get this in class, then email one of us.

For students who want to dip into the professional literature, there are links labeled "optional".

1. Probability  [16 January 2024 09:40:12.] 

   • Rogers. Just enough probability.

2. Partitioning variance  [11 January 2024 12:26:38.] 

3. Genomes and variation  [19 January 2024 16:26:50.] 

   • Gillespie sections 1.0-1.3

   Optional

   • Pritchard sections 1.1-1.4

   • Coop Chapter 1 and Chapter 2, through section 2.1.1

   • 1000 Genomes. 2010 A map of human genome variation from population-scale sequencing.

   • 1000 Genomes. 2012 An integrated map of genetic variation from 1,092 human genomes.

   • 1000 Genomes. 2015 A global reference for human genetic variation.

   • Halldorsson et al. 2022 The sequences of 150,119 genomes in the UK Biobank.

4. Random mating  [23 January 2024 09:24:07.] 

   • Gillespie section 1.4

5. Decay of heterozygosity  [04 January 2024 12:11:21.] 

   • Gillespie sections 1.4, 2.0-2.2

6. Mutation versus drift  [25 January 2024 09:11:48.] 

   • Gillespie section 2.3

   Optional

   • Coop sections 4-4.1.1

   • Pritchard sections 1.5, 2.1

7. Describing DNA sequence variation  [30 January 2024 18:06:11.] 

   • Rogers. Lecture notes on gene genealogies. Ch. 1.

8. Gene genealogies  [06 February 2023 15:28:05.] 

   • Rogers. Lecture notes on gene genealogies. Chs. 4-5.

   • Gillespie section 2.6

9. Python  [08 February 2024 08:16:28.] 

10. Site frequency spectrum  [08 February 2024 14:54:27.] 

    • Rogers. Lecture notes on gene genealogies. Ch. 6.

    Optional

    • Rogers and Wooding. 2021 Expectation of the site frequency spectrum.

11. Mismatch distribution and population growth  [08 October 2015 20:56:42.] 

    • Rogers. Lecture notes on gene genealogies. Ch. 7.

12. Population growth  [09 February 2023 10:30:58.] 

13. The neutral theory of molecular evolution  [20 February 2024 09:59:51.] 

    • Gillespie section 2.4-2.5

14. Selection  [23 February 2024 14:55:20.] 

    • Gillespie sections 3.0-3.3

    • Not quite enough selection Not quite enough selection (or perhaps a bit too much).

    Optional

    • Pritchard sections 2.5-2.7

15. When bad things happen to good genes: mutation vs selection  [27 February 2024 09:22:15.] 

    • Gillespie section 3.4

    • Fu 2013

16. Genetic load  [27 February 2024 09:22:27.] 

    • Gillespie section 3.5

17. Fixation of mutations  [28 February 2024 16:02:58.] 

    • Gillespie sections 3.9-3.10

    • Islands simulation

18. Neutral evolution at two loci  [30 March 2020 10:53:34.] 

    • Gillespie sections 4.0-4.1

19. Selection two loci  [30 March 2020 10:55:04.] 

    • Gillespie section 4.2

20. Why LD helps us find selective sweeps  [13 March 2020 17:19:51.] 

    • Rogers. 2018 Why LD hels us find selective sweeps.

21. Inbreeding  [24 March 2020 13:20:35.] 

    • Gillespie, sections 5.0-5.2

22. Inbreeding, drift, and fitness  [19 March 2024 09:59:13.] 

    • Gillespie, section 5.3

23. Population structure  [05 April 2020 15:52:46.] 

    • Gillespie, section 5.5.

    • Rogers, 2020. Geographic population structure.

    Optional

    • Pritchard section 2.4

24. Population structure part 2  [25 March 2024 16:35:18.] 

25. Detecting natural selection with genomic data  [26 March 2024 16:20:51.] 

    • Vitti et al

    • Hejase et al 2020 Summary statistics to gene trees: methods for inferring positive selection.

26. Genetic draft  [25 March 2024 16:45:30.] 

    • Gillespie section 4.3.

27. Population history from whole genomes  [02 April 2024 08:45:27.] 

    • Li and Durbin

    Optional

    • Rogers 2024

28. Archaic genes in modern humans  [04 April 2024 10:09:01.] 

    • Rogers. 2022. Using genetic data to build intuition about population history.

    Optional

    • Mendez et al, 2012 Global Genetic Variation at OAS1 Provides Evidence of Archaic Admixture in Melanesian Populations.

    • Vernot and Akey, 2014 Resurrecting surviving Neandertal lineages from modern human genomes.

    • Castellano et al, 2014

29. QTs 1: genes and environment  [08 April 2024 16:05:19.] 

    • Gillespie, sections 6.0-6.1

30. QTs 2: heritability  [12 April 2024 10:35:31.] 

    • Gillespie, sections 6.0-6.1

31. QTs 3: response to selection  [08 April 2024 16:04:34.] 

    • Gillespie, section 6.2

    • Response to selection on quantitative traits

32. Trait mapping  [16 April 2024 17:03:44.] 

    • Tam et al. 2019 Benefits and limitations of genome-wide association studies.

    • Uffelmann et al 2021 Genome-wide association studies.

33. Missing heritability: trait prediction and prospects for personalized medicine

    • Manolio et al. 2009 Finding the missing heritability of complex diseases

    • Polygenic risk scores

    • Massarat et al. 2023 Human pangenome supports analysis of complex genomic regions

    Optional

    • Liao et al 2023 A draft human pangenome reference.

    • Povysil et al. 2019 Rare-variant collapsing analyses for complex traits: guidelines and applications.

    • Choi et al. 2020 Tutorial: a guide to performing polygenic risk score analyses.

34. Genome-Wide Association Studies (GWAS)  [18 April 2024 14:59:34.] 

35. Evolution of quantitative traits  [23 April 2024 18:17:12.] 

    • Barghi et al. 2020 Polygenic adaptation: a unifying framework to understand positive selection.