Ecology (L567) 2015
Department of Biology,
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, 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
The course will be offered
again during the Fall semester of 2015. Typically, the
class meetings are part lecture and part discussion in an
syllabus for 2015
FIRST EXAM (13 October)
Study questions for first exam: part 1. 2015
updated on 21 Sept 2015.
Study questions for first exam:
part 2. 2015
(pdf) <--last updated 01 October 2015.
questions for second exam, 2015 Second EXAM (3
<--last updated on
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))
mean, variance, covariance, & regression ( online handout)
Optional reading: Peters RH :
Tautology in ecology and evolution
The origins of theoretical population genetics (see Provine's
Optional: Michod's paper on positive
heuristics in evolutionary biology
Lecture 3: Basic Population
Genetics. Overheads for
Optional: Fisher's classic 1918
paper on the correlation between relatives.
Strongly recommended: c omputer-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.
Simulation Instructions to download the
worksheet. After you fill out the
worksheet, you can compare your answers to Answers to
for qhat (mathematica
mutation-selection balance example. Here is the solution
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: Overheads for Selection differential vs the selection
gradient: towards a more general formulation. Quantitative Genetics: Breeder's
names for population genetics and quantitative genetics
of linear regression (by James Kirchner)
Optional: critique of the Breeder's
equation ( pdf).
genetics excel workbook
Partitioning the variance. Breeding values and additive
genetic varianceOverheads for
and V A D (mathematica
Here is the solution as html.
Optional: Excel spreadsheet calculation of BreedingValues
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 :
Frequency-dependent selection and game theory.Overheads for
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
1978. Animal Behaviour 26:138-147
Lecture 7: Mixed
vs. Conditional StrategiesOverheads for
Lecture 8: Logic of animal conflict; RockPaperScissors
Overheads for Class discussion of Davies 1978
optional: Lively's excel model for
hawk-dove game H-D
Optional: update on the
Davies study ( pdf).
Paper Scissors paper (Nature 1996)
Lecture 9: Games against the field:
the Fisherian sex ratioOverheads for
Fisher's sex ratio: Graph the CSS: Mathematica
For help with calculus see S.P.
Thompson, "Calculus made easy" Third edition (QA303.T45)
Lecture 10: Local
mate competitionOverheads for
Color overheads for the LMC model.
optional reading: Hamilton
(1967) extraordinary sex ratios
Links to the local mate
competition model ( Mathematica
notebook file )
and ( pdf file ).
exercise for understanding local mate competition:
and download excel
Optional: local mate
experimental study with barnacles.
reading for lecture 11: Salmon paper by Einum&Fleming
(2000) Nature 405:565-567.
11: Life-history theory: size-number compromises and geometric
mean fitness. Plus discussion of Einum and Fleming paper.Overheads for
Recommended: Link to the Lloyd's
size-number model ( Mathematica
file) and ( pdf
to Smith-Fretwell model as excel
Optional, Steve Stearns'
paper on Geometric Mean Fitness
experimental evolution paper on bet hedging ( pdf).
Bet hedging excel
Lecture 11.5: Evolution
Overheads for Lecture11.5
<---------------------------End of material for first
has been updated for 2015
Lecture12: Cost of sex, Muller's ratchet and Kondrashov's
Overheads for Lecture12
ratchet and the hatchet overheads.
to excel worksheet for Poisson distribution of new
Lecture13: The ecological hypotheses
for sex.Overheads for
Read Burt &
Bell 1987 for class on Thursday 10 October.
Optional reading: The
Red Queen from Bell (1982) The masterpiece of
-----------------------End of material
for first exam---------------
Lecture14: Testing the ecological hypotheses (Burt and
Bell), Difficulties on theory, Pluralism. Overheads contained in "overheads for lecture 13-14" above. (Most of this
was an informal talk after the first exam.)
Optional reading: Pluralistic hypotheses The
ratchet and the red queen in Nature 1994
Epistasis, Linkage Disequiblium,
Recombination, Runaway sexual selection Lecture
Overheads for Lecture14-15
Suggested reading Kirkpatrick
(1982) in Evolution
on the evolution of female choice.
(1982) in Nature. Female choice in
Lecture 16-17. Sexual selection, chase-away selection,
Overheads for Lecture
Optional (but highly suggested)
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.
al. 2001: MHC-dependent choice in fish.
Optional reading: interaction-independent sexual
Suggested reading: Wilkinson
& Reillo 1994. Correlated selection for female
preference in stalk-eyed flies. (see also Wilkinson et al 1998,
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
And in salmon:
Scanned overheads: examples
of meiotic drive (not shown for 2013)
Read: reproductive mode
and speciation Zeh&Zeh
Optional: Zeh&Zeh 2008
Optional: Rice (1996)
paper on conflict between the sexes
Lecture18-19 . Social
evolution, kin selection.Overheads for
For 11 Nov 2010: Overheads for derivation
of the Taylor&Frank method
Frank's paper on how to model kin selection (optional) Lecture
Adaptation and integration of evolutionary forces
Overheads for lecture
on integration of evolutionary forces.
from malaria lecture showing changes in the adaptive
surface with inbreeding ( pdf of 3D
Mathematica file for
invasion of S and C alleles.
Lively's excel simulation spread of S
and C alleles with and without inbreeding
output for excel simulation model.
Lecture21: Group selection,
Population structure, Effective population size (Ne), and
shifting balanceOverheads for
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
of Price equation for L567
Lecture22 : The ecology of speciation IOverheads for
Read for lecture/discussion 23: Saetre
al. Nature: sexually selected character displacement in a
Lecture23 : The ecology of speciation II
Overheads for lecture23
overheads stickleback fish for lecture 23
( ) News and
Views on Saetre et al. paper.
points for Saetre et al for lecture 23
of pollinator mediation of prezygotic isolation Schemske
Overheads for lecture24
paper on macroevolution in gastropods.
Orr's paper on the evolutionary genetics of speciation
MJ Wade's paper
on a gene's eye view of speciation
Second EXAM (3 December)
of material for second
Lecture 25 review for final
Lecture 26: guest lecture by Levi Morran
Eco-evolutionary feedbacks and the fundamental
theorem of natural selection
of plasticity (not covered)
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.
is an example. Here
is another example.
And possible chalk talk on the evolution of
. correlated trait
evolution as pdf file.
suggested reading is support of Delph lecture
Read for Tuesday, December
Lecture24 (9DEC08: Loose ends. Class discussion of
Schemske and Bradshaw)
Lecture 25 (): special topic?
C. M. Lively, Dept.
of Biology, Indiana University
Go back to Lively's homepage .