Evolutionary Ecology (L567) 2015

Department of Biology, Indiana University

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.

FIRST EXAM (13 October)

Study questions for first exam: part 1. 2015
(pdf) <--last
updated on 21 Sept 2015.

Study questions for first exam:
part 2. 2015
(pdf) <--last updated 01 October 2015.

Second EXAM (3
December)

Study
questions for second exam: part 1.
2015 <--last updated on
19 Nov 2015

Lecture 1: Early history of evolutionary thought: the Darwinian revolution

(see books by Michael Ruse and E. Mayr (refs in syllabus))

Overheads for Lecture1

mean, variance, covariance, & regression (online handout)

Optional reading: Peters RH: Tautology in ecology and evolution

Overheads for Lecture2

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

Overheads for Lecture3

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

Strongly recommended: computer-simulation exercises in population genetics. For L567 students (2015) see "population genetic exercises" on Oncourse. There are two exercises to complete.

If you are not part of the course, an alternative version can be found as follows. 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.

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 8 Sept 2015. 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).

Optional: Quantitative genetics excel workbook

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

Overheads for Lecture5

Optional: solution for VA and VD (mathematica notebook). Here is the solution as html.

Optional: Excel spreadsheet calculation of BreedingValues

Note: Excel Population/Quantitative-Genetic exercise #2 due 15 Sept 2015. There will be "individual differences" in formatting, but hand in 3 pages (or more) that have the info contained in this example.

Optional reading on Multivariate Selection:

Arnold, 1994

Overheads for Lecture6

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, Thurs, 17 Sept 2015

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: Fisher's sex ratio: Graph the CSS: Mathematica notebook. pdf 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 file) and (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.

Overheads for Lecture11.5

-------------------------------End of material for first exam---------------------------

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.

Overheads for Lecture13-14

Read Burt & Bell 1987 for class on Thursday, October 15th.

Optional reading: The Red Queen from Bell (1982) from, The Masterpiece of Nature: the Evolution and Genetics of Sexuality

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

Overheads for Lecture 16-17

Read: reproductive mode and speciation Zeh&Zeh 2000

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 2015)

Optional: Zeh&Zeh 2008

Optional: Rice (1996) paper on conflict between the sexes

Lecture18-19. Social evolution, kin selection.

Overheads for lecture 18-19

Axelrod & Hamilton's paper on tit-for-tat (optional)

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

Lecture21-22: Group selection, Population structure, Effective population size (Ne), and shifting balance

Overheads for shifting balance: lecture21

Overheads for group selection, Price equation: lecture22

Optional reading: the Price Equation by A. Gardner

Optional: for a derivation of the Price equation see (Frank, S. 2012) J. Evol. Biol. 25:1002-1019

Optional: on the relationship between group selection and kin selection. Lehmann et al PNAS

Lecture23: The ecology of speciation I

Overheads for lecture23

Read for lecture/discussion 24: Saetre et al. Nature: sexually selected character displacement in a flycatcher.

(Optional: News and Views on Saetre et al. paper.)

Lecture24: The ecology of speciation II

Overheads for lecture24

optional reading: pollinator-mediated prezygotic isolation

Schemske and Bradshaw PNAS

Overheads for lecture25

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

Lecture 26: Eco-evolutionary feedbacks and the fundamental theorem of natural selection

Overheads for lecture26

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

Lecture 27 review for final

Lecture 27:

Plasticity: developmental conversion

more of plasticity (not covered)

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.

Overheads. correlated trait evolution as pdf file.

suggested reading is support of Delph lecture Arnold, 1994

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

Go back to Lively's homepage.