Evolution (L567)
Department of Biology,
Indiana University
Graduate
evolution (L567).--This
is a graduate course in evolution, focusing on the theoretical
underpinnings. Topics include basic quantitative genetics, basic
population genetics, genetic drift, life-history theory, evolution
of sex, sexual selection, mutation-selection balance, genetic
load, evolution of social behavior, correlated responses to selection,
speciation, macroevolution, and phylogenetic reconstruction. Graduate
standing or permission of the instructor required. Advanced
undergraduates
in Biology are welcome.
The course will be offered
again during the Fall semester of 2006.
Course
syllabus for 2006 as html
Course
syllabus for 2006 as a pdf file
Click here to go to library
electronic-reserves service
Study
questions for first exam, 2006 <--updated
5 October 2006
Study
questions for second exam, 2006<--updated 22 November 2006 (final
update)
<>Readings
and
exercises in support of lecture material
Brief History and Philosphy of
Evolutionary Biology
1. Overheads from first
lecture 29 Aug., 2006 (pdf).
2. Optional reading: Peters (1976) Tautology
in Evolution and Ecology (1.3mb).
3. Optional: 2004 Lecture by Prof. Lynda Delph on History
of Evolutionary thought (same file in pdf
format).
Population Genetics/Quantitative
genetics
1. Overheads
from second lecture (pdf), 31 Aug 2006.
2. Optional (but highly recommended) computer exercise in
population genetics. Click on Pop.
Gen. Simulation Instructions (revised 6 Sept 06) to download the
worksheet.
After you fill out the
worksheet, you can compare your answers to Answers to
PopGen exercise. Make sure you run through the exercise above
before looking
at the answers.
3. Overheads
from third lecture (pdf), 5 Sept., 2006
4. Optional: reading for history and philosophy: Michod, 1981
5. Optional: solution
for qhat (mathematica notebook) in the mutation-selection balance example. Here is the
solution as html.
Read these 2 papers below for Tuesday, Sept. 12, 2006
6. Boag
and Grant,
1981
7. Weis and
Abrahamson, 1986
8. Overheads
for lecture 4 (pdf), 7 Sept., 2006
9. Response
to selection (pdf file), a graphical presentation from
Futuyma's book.
10. Optional: Intro
to QG lecture (powerpoint) by Dr. Farrah Bashey-Visser
11. lecture
5 (pdf), 12 Sept 2006
12a. Optional: excel worksheet on variance
in breeding values
12b. Optional:
mathematica
notebook or html
showing that V(A)=variance in breeding values = 2pq[a + d(q - p)]2
13. Maynard
Smith chapter on QG from Evolutionary Genetics (Optional. Note: pages 112 and 113 are out of order)
14. Grant and
Grant 1995 optional paper on testing QG theory with Darwin's
finches.
14.5. Mathematics
of correlated trait evolution as pdf file
Extra credit problems...
Popgen assignment
1. Lively's excel
worksheet.
Popgen assignment 2. Lively's excel
worksheet.
Evolutionary Game theory.
14. lecture
6 (pdf), 14 Sept 06
15. Davies,
N.B. 1978. Animal Behaviour 26:138-147 (Read for 19 Sept.)
16. Maynard
Smith's chapter on the basic model (highly
recommended)
17. lecture
7 (pdf), 19 Sept 06
18. Real-life rock-paper-scissors
(optional paper by Sinervo&Lively).
19. Sinervo's
"Lizard Land" website contains videos
of the lizards
20. lecture
8 Part 1 (pdf), 21 Sept 06 (conclusion of discrete
strategies.)
21. lecture
8 Part 2 (pdf), 21 Sept 06 (calculus-refresher overheads,
pdf
file, 2.3mb.)
22. For help with calculus see S.P. Thompson, Third edition
(QA303.T45)
23. lecture
9 pdf. 26 Sept 06. Continuous strategies: Fisherian Sex
ratio.
24. lecture
10 pdf. 28 Sept 06. Local Mate
Competition.
25. LMC_overheads.
Color overheads for the LMC model (3.1 mb).
26. Extra credit assignment due Oct. 5th (1 point). create
an excel worksheet that calculates and graphs Fitness against
allocation to male function, ai, as a function of the number of mates,
and the residents allocation to male function. place on the
graph, the resident's allocation, and the ESS. Here is an
example. Even if you don't do the extra credit, it would be
good to look at the example. Note especially how the fitness
surface changes at the population moves toward the ESS.
26.5 Optional. Fisher's sex ratio: Graph the CSS: Mathematica notebook. pdf file.
27. Local
Mate Competition model
(Mathematica notebook. You need Mathematica to run it).
Local mate competition model
output as pdf file
28. Hawk-dove dynamics. pdf example.
excel
worksheet.
Life-history Theory and more on LMC.
31. Required reading: Salmon paper by Einum&Fleming
(2000) Nature 405:565-567.
32. Size Number Theory
(Mathematica notebook. You need Mathematica to run it).
Model
output as pdf file
33. Lecture
11 pdf.
34. Optional HPS reading: Stearn's paper
on geometric mean fitness
35. Optional reading on Local Mate Competition: Raimondi&Martin
1991.
36. Optional: John Maynard Smith's review
of sex ratio evolution/gender allocation (see pages 251-258)
37. Size number model
worked (pdf)
Breeding system evolution
38. Lecture 12 pdf (cost and benefits of sex)
39. Local mate competition assignment (extra
credit 3). Lively's
excel worksheet.
40. the
ratchet and the hatchet overheads. added 10 Oct. 2006.
------
Exam 1 material above this line.
--------
Evolution
of sex, cross
fertilization, and recombination
41. Typed
overheads from lecture 13.
42. Additional
overheads from lecture 13.
43. Required reading: Burt and
Bell 1987. A test of two theories of recombination.
44. Optional: Pluralistic hypothesis The
ratchet and the red queen in Nature 1994
44.5 Optional: Review of the ecological
genetic theories of sex.
Linkage disequilibrium, epistasis and
recombination
45. Overheads
from lecture 14,
19 October 2006
46. Excel worksheet:
the effect of selection and recombination on linkage disequilibrium
Female choice, linkage disequilibrium
and sexual selction
47. Overheads
from lecture 15, 24 October 2006
48. Kirkpatrick
(1982) in Evolution on
the evolution of female choice.
49. Wilkinson
& Reillo 1994: Correlated selection for female preference
in stalk-eyed flies. (see
also meiotic drive in stalk-eyed flies below)
Wilkinson's
overview of stalk-eyed flies. Wilkinson's web
page.
50. Wedekind
et al 1995: MHC-dependent choice in humans (html
version) Optional reading
51. Reusch
et al. 2001: MHC-dependent choice in fish. Optional reading
52. Overheads
from lecture 16, 26 October 2006.
Selfish genetic elements
53. Typed
overheads from lecture 17, 31 October 2006.
53.5 More
overheads from lecture 17 (scanned overheads).
54. Wilkison
et al. 1998. Nature: meiotic drive suppression in stalk-eyed
flies (see also Wilkinson
& Reillo in sexual selection)
55. Review of meiotic drive suppression by Pomiankowski
& Hurst 1999 in TREE
56. Beeman
et al. 1992. The MEDEA gene in flour beetles. (News
and Views commentary on Beeman et al.)
57. Hurst
& Werren 2001 review of selfish genetic elements in Nature
Genetics
58. Skinner's discovery
of psr in Heredity
Sexual conflict
59. Rice
(1996) paper on genetic conflict between the sexes
60. Overheads
from lecture 18 (2 Nov. 06):
61. Read for class discussion: reproductive mode and
speciation Zeh&Zeh 2000
Kin selection and
cooperation
62.
Overheads
for lecture 19, Thusday November 7th: Prisoner's delimma,
read Turner & Chao 1999*
(*See also the News and Views by Nowak
and Sigmund 1999)
63. Kin selection (optional): Taylor
and Frank
1996. How to make a model of kin selection.
(See also Steve
Frank's homepage)
64. Derivation of the Taylor and Frank (1996)
model for kin
selection
(word file)
(pdf
file)
Adaptation and integration of evolutionary forces
65. Templeton's
paper on integration
of evolutionary forces.
66. Overheads
from lecture 20 (9 Nov 2006)
67. Graphs from malaria
lecture showing changes in the adaptive surface with inbreeding.
68. Mathematica
file for invasion
of S and C alleles.
69. jpg file showing results
for spread of S and C alleles with and without inbreeding
Shifting balance and Speciation
For 2008 read Wade
MJ 2002: epistasis, selection and speciation
70. Lecture 21, Tues Nov 14th: chalk talk (see your
notes). No overheads.
71. Read for Thurs(Nov 16th 2006) shifting balance paper by Wade,
MJ 1992
72. Lecture
22 typed overheads, speciation I
(16 Nov 06). scanned
graphs
73. Read for Tues, 21 Nov 06.
Saetre
et al. Nature 2000: sexually selected character displacement
in a flycatcher. (News
and Views on Saetre et al. paper.)
and
Schemske
and Bradshaw PNAS 1999: Evolution of floral traits in monkey
flowers.
(See http://www.plantbiology.msu.edu/schemske.shtml
for photos of hybrids and overview of Schemske lab.)
Optional readings for speciation
74. Hendry
et al. Nature 2000: Rapid evolution of reproductive isolation
in salmon.
75. Buckling
and Rainey 2002: Role of parasites in sympatric and
allopatric
host diversification<--
New
76. Coyne and
Orr 1998: Evolutionary genetics of speciation<-- lecture 22 taken mostly from this
one
77. Lecture
23, scanned graphs of speciation in stickleback fish (Tues., 21 Nov
06).
------
Exam 2 material above this line. Last update: 08 November 2006
--------
Macroevolution
1. Jablonski's
1986 paper on speciation/extinction in marine invertebrates.
2. Macroevolution: scanned
overheads from last lecture (7 Dec. 2006)
3. Math underlying verbal arguement for: QG
of correlated traits
Typed version of above as
pdf file
------ Finishing touches above this line. Last update: 07
December 2006
--------
Not
used in 2006 below
Quantitative Genetics
3. Arnold, 1994
(optional)
4. Handout on
Basic QG
6. Optional: Changes
in the G matrix. Optional MS by Agrawal, Brodie & Rieseberg
publishished in Genetica 112-113: 33-43.
11. Transition from
breeder's equation for one trait to delta zbar for multiple traits
as pdf file <--new Nov04
12.
5. Evolution of virulence. Handout on maximizing R0.<--new Nov.
29th, 2004
Host-parasite coevolution
1. Lively&Dybdahl 2000: Rare
advantage experiment in snails
2.
3.
Sexual selection
4. Siva-Jothy
2000: A mechanistic link between sexual selection and a
parasite-resistance
trait
5. Andrew Cockburn's review of Lande's
model on run-away sexual selection
6. John Maynard Smith's review of Sexual
selection and Kirkpatrick's model of the run-away process
(see pages 258-264)
7. Random mating vs. Condition-Dependent Choice vs. Opposites
Attract: Howard&Lively
in press BMC Evol.Biol.
8.
9.
Levels of selection
6. Price equation: Queller's
general model for kin selection <--new Nov04
7. Derivation of the Taylor and Frank model for kin selection
(word file)
8.
9.
4. M.
Wade's 1996 paper on kin selection and population structure
(includes discussion of
effect of VAR in offspring production on effective population
size).
5. Mathematica file for invasion
of S and C alleles.
6. jpg file showing results
for spread of S and C alleles with and without inbreeding
7. Overheads
on shifting balance theory. <--added
1 Dec., 2004
8.
Genetic correlations and evolution along genetic lines of least
resistance
1. Schluter's chapter
on lines of least resistance
2. Overheads: QG
of correlated traits
3. Typed version of
overheads as pdf file
4.
C.
M. Lively, Dept. of Biology, Indiana University
Go back to Lively's homepage.
