Evolution (L567) 2013
Department of Biology, Indiana University


Graduate evolution (L567).--This is a graduate course in evolution, focusing on the theoretical underpinnings.  Beginning in 2010, I have put more focus on Evolutionary Ecology and Behavioral Ecology.  The goal will be to complement our graduate courses in Evolutionary Genetics.  Topics will include life-history theory, evolution of sex, sexual selection, evolution of social behavior, evolution of virulence, and the evolutionary ecology of speciation and macroevolution. I also plan to cover some of the basic theory for Population Genetics and Quantitative Genetics.  Graduate standing or permission of the instructor is required. Advanced undergraduates in Biology are welcome. 

The course will be offered again during the Fall semester of 2015.  Typically, the class meetings are part lecture and part discussion in an informal atmosphere. 


Course syllabus for 2013

Grading Policy



Study questions for first exam, 2013 (pdf) <--updated 1 October 2013

Study questions for second exam, 2013 <--updated 24 November 2013

<>Readings and exercises in support of lecture material

Lecture 1: Early history of evolutionary thought: the Darwinian revolution
(see books by Michael Ruse and E. Mayr (refs in syllabus))

Overheads for Lecture1
First-day Quiz link
mean, variance, covariance, & regression (online handout)

Optional reading: Peters RH: Tautology in ecology and evolution

Lecture 2: The origins of theoretical population genetics (see Provine's book)

Overheads for Lecture2

Optional: Michod's paper on positive heuristics in evolutionary biology

 
Lecture 3: Basic Population Genetics.  

Overheads for Lecture3

Optional: Fisher's classic 1918 paper on the correlation between relatives.

Optional (but highly recommended) computer exercise in population genetics.  Click on Pop. Gen. Simulation Instructions 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.

Optional: solution for qhat (mathematica notebook) in the mutation-selection balance example.  Here is the solution as html

Note: Excel Population-Genetic exercise #1 due 12 Sept 2013.  There will be "individual differences" in formatting, but hand in 3 pages that have the info contained in this example.



Lecture 4: Quantitative Genetics: Breeder's equation.
Selection differential vs the selection gradient: towards a more general formulation. 

Overheads for Lecture4


Variable names for population genetics and quantitative genetics

Optional: derivation of linear regression (by James Kirchner)

Optional: critique of the Breeder's equation (pdf).

 
Lecture 5: Partitioning the variance.  Breeding values and additive genetic variance

Overheads for Lecture5

Optional: solution for VA and VD (mathematica notebook) in the mutation-selection balance example.  Here is the solution as html

Optional: Excel spreadsheet calculation of BreedingValues

More advanced. correlated trait evolution as a pdf file.

Lecture 6: Frequency-dependent selection and game theory.
Overheads for Lecture6


Note: Excel Population/Quantitative-Genetic exercise #2 due 24 Sept 2013.  There will be "individual differences" in formatting, but hand in 3 pages (or more) that have the info contained in this example.

For today's meeting, read: Maynard Smith's chapter on the basic game-theory model (highly recommended)
Or go here for the whole book, which is available online to IU students.

Read for Lecture 8, Tuesday, 19 Sept 2013
Davies, N.B. 1978. Animal Behaviour 26:138-147



Lecture 7: Mixed vs. Conditional Strategies

Overheads for Lecture7



Lecture 8: Logic of animal conflict; RockPaperScissors

Class discussion of Davies 1978
 
Overheads for Lecture8

optional: Lively's excel model for hawk-dove game H-D game

Optional: update on the Davies study (pdf).


Optional: Rock Paper Scissors paper (Nature 1996)




Lecture 9: Games against the field: the Fisherian sex ratio

Overheads for Lecture9 (pdf)


optional: first and second derivatives(pdf)
optional: Fisher's sex ratio: Graph the CSS:  Mathematica notebookpdf file.

For help with calculus see S.P. Thompson, "Calculus made easy" Third edition (QA303.T45)





Lecture 10: Local mate competition

Overheads for Lecture10 (pdf)
LMC_supplement.  Color overheads for the LMC model.

optional reading: Hamilton (1967) extraordinary sex ratios


Recommended.   Links to the local mate competition model (Mathematica notebook fileand (pdf file).


Optional exercise for understanding local mate competition: download directions and download excel calculations.

Optional: local mate competition, an experimental study with barnacles
 
Required reading for lecture 11: Salmon paper by Einum&Fleming (2000) Nature 405:565-567.

Lecture 11: Life-history theory: size-number compromises and geometric mean fitness.  Plus discussion of Einum and Fleming paper.

Overheads for Lecture11


Recommended: Link to the Lloyd's size-number model (Mathematica file) and (pdf file)

optional: Link to Smith-Fretwell model as excel file 

Optional, Steve Stearns' paper on Geometric Mean Fitness


Optional: experimental evolution paper on bet hedging (pdf).

Bet hedging excel worksheet. 


Lecture12: Cost of sex, Muller's ratchet and Kondrashov's hatchet.

Overheads for Lecture12
the ratchet and the hatchet overheads

Link to excel worksheet for Poisson distribution of new mutations.


Remember: FIRST EXAM (15 October 2013)


Lecture13: The ecological hypotheses for sex.

Overheads for Lecture13-14


Read Burt & Bell 1987 for class on Thursday 10 October.


Optional reading: The Red Queen from Bell (1982) The masterpiece of nature. 


-----------------------End of material for first exam---------------
 
Lecture14: Testing the ecological hypotheses (Burt and Bell), Difficulties on theory, Pluralism. (Most of this was an informal talk after the first exam.)
 
Overheads contained in "overheads for lecture 13-14" above.

Optional reading: Pluralistic hypotheses The ratchet and the red queen in Nature 1994


Lecture 14-15.  Epistasis, Linkage Disequiblium, Recombination, Runaway sexual selection

Overheads for Lecture14-15

Suggested reading  Kirkpatrick (1982)  in Evolution on the evolution of female choice.
Suggested reading  Andersson (1982)  in Nature.  Female choice in widow birds.


Lecture 16-17.  Sexual selection, chase-away selection, parent-parent conflict


Overheads for Lecture 16-17

Optional (but highly suggested) reading: Hamilton and Zuk (1982)
Optional reading: Sexual selection in plants (it happens): Delph and Ashman 2006
Optional reading:Wedekind et al 1995: MHC-dependent choice in humans.
Optional reading. Reusch et al. 2001: MHC-dependent choice in fish.
Optional reading: interaction-independent sexual selection: Murphey 1998

Suggested reading: Wilkinson & Reillo 1994. Correlated selection for female preference in stalk-eyed flies. (see also Wilkinson et al 1998, below)
Suggested reading.  Wilkinson et al. 1998. Nature: meiotic drive suppression in stalk-eyed flies
(see also Wilkinson & Reillo 1994)

From Fabio: More on MHC-mediated mate choice in humans
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100018

And in salmon:
http://www.academia.edu/371140/MHC-mediated_mate_choice_increases_parasite_resistance_in_salmon



Scanned overheads: examples of meiotic drive (not shown for 2013)
Read: reproductive mode and speciation Zeh&Zeh 2000
Optional:  Zeh&Zeh 2008
Optional: Rice (1996) paper on conflict between the sexes



Lecture18-19.  Social evolution, kin selection.
Overheads for lecture 18-19
For 11 Nov 2010: Overheads for derivation of the Taylor&Frank method
Taylor & Frank's paper on how to model kin selection (optional)


Lecture 20:
Adaptation and integration of evolutionary forces


Overheads for lecture 20

Templeton's paper on integration of evolutionary forces.
 
3D graphs from malaria lecture showing changes in the adaptive surface with inbreeding (pdf of 3D graphs).
Mathematica file for invasion of S and C alleles.
Lively's excel simulation spread of S and C alleles with and without inbreeding

pdf output for excel simulation model.



Lecture21: Group selection, Population structure, Effective population size (Ne), and shifting balance
Overheads for lecture21
Optional reading: the Price Equation by A. Gardner
Advanced: for a derivation of the Price equation see (Frank, S. 2012) J. Evol. Biol. 25:1002-1019

Derivation of Price equation for L567


Lecture22: The ecology of speciation I
Overheads for lecture22



Read for lecture/discussion 23: Saetre et al. Nature: sexually selected character displacement in a flycatcher.


Lecture23: The ecology of speciation II

Overheads for lecture23
scanned overheads stickleback fish for lecture 23

(News and Views on Saetre et al. paper.)
Discussion points for Saetre et al for lecture 23
reading of pollinator mediation of prezygotic isolation: Schemske and Bradshaw PNAS


Lecture24: Macroevolution
Overheads for lecture24
Jablonski's paper on macroevolution in gastropods.
Coyne and Orr's paper on the evolutionary genetics of speciation
MJ Wade's paper on a gene's eye view of speciation


       <----------------------End of material for second exam--------------->


Lecture 25 review for final

Lecture 26: guest lecture by Levi Morran

Lecture 27:
Eco-evolutionary feedbacks and the fundamental theorem of natural selection
Plasticity: developmental conversion

more of plasticity (not covered)

<------------------ overhead slides updated to here for 2013 ----------------------->



not covered in 2013

Exercise 4, due Nov. 2nd: create an excel worksheet that calculates epistasis for fitness, the generation of linkage disequilibrium, and the effect of recombination on linkage disequilibrium.  Turn in three sheets, each one for different parameter values.  Use parameters different from the ones in my examples.  Here is an example
Here is another example.

And possible chalk talk on the evolution of virulence.


Overheads
. correlated trait evolution as pdf file.
suggested reading is support of Delph lecture Arnold, 1994





Read for Tuesday, December 9th: Schemske and Bradshaw PNAS

Lecture24 (9DEC08: Loose ends.  Class discussion of Schemske and Bradshaw)

Lecture 25 (): special topic?



C. M. Lively, Dept. of Biology, Indiana University
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