Evolution (L567) 2010
Department of Biology,
Indiana University
Graduate
evolution
(L567).--This
is a graduate course in evolution, focusing on the theoretical
underpinnings. Beginning in 2010, I will focus the course more on
Evolutionary Ecology and Behavioral Ecology. The goal will be to
complement Dr. Montooth's graduate course 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 2012. Typically, the class
meetings are part lecture and part discussion in an informal
atmosphere.
Course
syllabus
for
2010
Grading Policy
Study questions for 2008
Study
questions for first exam, 2010 (pdf) <--updated 6 October 2010
Study
questions for second exam, 2010<--updated
26
November
2010
<>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)
Overheads for Lecture1
First-day Quiz
mean, variance, covariance, & regression (online handout)
Optional reading: Peters RH: Tautology in
ecology and evolution
Lecture 2: The origins of theoretical
population genetics (see book by Povine)
Overheads for Lecture2
Lecture
3: Basic Population Genetics. Quantitative Genetics: Breeder's
equation.
Overheads for Lecture3
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
14
Sept
2010.
There
will
be
"individual
differences"
in
formatting,
but
hand
in
3
pages
that
have
the
info
contained
in
this
example.
Optional: critique of the Breeder's equation (pdf).
Lecture 4: Selection
differential vs the selection gradient: towards a more general
formulation.
Overheads for Lecture4
Lecture
5: 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
Lecture 6 (16
Sept):
Frequency-dependent selection and game theory.
Overheads for Lecture6
Note: Excel
Population/Quantitative-Genetic
exercise
#2
due
21
Sept
2010.
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)
Read for lecture 7, Tuesday, 21 Sept 2010
Davies,
N.B. 1978. Animal Behaviour 26:138-147
Lecture
7 (21 Sept 2010): Mixed vs. Conditional Strategies
Overheads for Lecture7
Lecture
8
(23
Sept
2010):
Logic
of
animal
conflict
(discuss
Davies
1978);
RockPaperScissors
Overheads for Lecture8
Part1
(pdf)
Overheads for Lecture8
Part2 (pdf)
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 (28 Sept 2010): Games against the
field: Fisherian sex ratio
Overheads for Lecture9
(pdf)
For help with calculus see S.P.
Thompson, "Calculus made easy" Third edition
(QA303.T45)
Lecture10 (30 Sept
2010): Local mate competition
Overheads for Lecture10
(pdf)
LMC_overheads.
Color
overheads
for
the
LMC
model
(3.1
mb).
Suggested reading: Hamilton
(1967)
extraordinary
sex
ratios
Optional (but
recommended).
Fisher's sex ratio: Graph the CSS: Mathematica notebook. pdf file.
Exercise 3, due
Oct. 7th:
create
an excel worksheet that calculates and graphs fitness against
allocation to male function, ai, as a function of the number of
mates. Include on the
graph both the resident's allocation and the ESS. Here is an
example.
New: highly
recommended. Links to the local mate
competition model (Mathematica file) and
(pdf file).
Required reading for lecture 11:
Salmon paper by Einum&Fleming
(2000)
Nature
405:565-567.
Lecture11
(5
October
2010):
Life-history
theory:
size-number
compromises
Overheads for Lecture11
Highly
recommended: Links to the size-number
model (Mathematica file) and (pdf file)
Optional, but highly recommended: Steve Stearns paper on
Geometric Mean Fitness
Optional: experimental
evolution of bet hedging (pdf).
Bet hedging excel
worksheet.
Lecture11(cont.) (7 October 2010):
Discussion of
Einum&Fleming. Temporal environmental variation and geometric
mean fitness.
(no new overheads)
-----------------------End of
material for first exam---------------
Lecture12(12 October 2010): Cost of sex; the Muller's ratchet and
Kondrashov's hatchet.
Overheads for Lecture12
the
ratchet and the hatchet overheads.
FIRST EXAM (14 October 2010)
Lecture13(19
October2010):
The
ecological
hypotheses
for
sex.
Overheads for Lecture13
More: Additional
color
overheads
from
lecture
13.
Read Burt & Bell
1987 for class on Thursday 21 October.
Lecture14
(21
October
2010):
Testing
the
ecological
hypotheses
(Burt
and
Bell),
Difficulties
on
theory, Pluralism.
Overheads
contained
in
"overheads
for
lecture
13"
above.
Optional reading:
Pluralistic hypotheses The
ratchet and the red queen in Nature
1994
Epistasis, Linkage Disequiblium, and Recombination
Overheads for Lecture14
Lecture15,
Linkage disequilbrium in sexual selection
Overheads for Lecture15
Suggested reading Kirkpatrick
(1982) in Evolution on
the evolution of female choice.
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.
Lecture16 (2 November 2010). Good
genes and the paradox of female choice
Overheads for Lecture16
Optional (but highly suggested) reading: Hamilton
and Zuk (1982)
Suggested reading: Sexual selection in plants (it happens): Delph
and
Ashman
2006
Suggested reading:Wedekind
et al 1995: MHC-dependent choice in humans.
Suggested reading. Reusch
et al. 2001: MHC-dependent choice in fish.
Suggested reading: interaction-independent
sexual selection: Murphey 1998
read for 9 November: reproductive mode
and
speciation Zeh&Zeh 2000
Lecture17
(4
Nov.
2010).
Sexual
selection,
genetic
correlations,
and meiotic drive in stalk-eyed
flies.
Overheads for Lecture17
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)
Suggested reading: Wilkinson's
overview of stalk-eyed flies. Wilkinson's web
page.
Suggested reading: interaction-independent sexual selection: Murphey 1998
Lecture18 (9 Nov.
2010) Sexual conflict, chase-away selection, selection arenas
Overheads (typed: Zeh&Zeh) for Lecture18
Scanned overheads: examples
of
meiotic
drive (not shown for 2010)
Read: reproductive mode and
speciation Zeh&Zeh 2000
Read for exam: Rice
(1996) paper on conflict between the sexes
Lecture19 (9
Nov. 2010): Social evolution, kin selection.
Overheads for lecture
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 (11 Nov. 2010): Adaptation
and
integration
of
evolutionary
forces
First, Taylor and Frank's model (see above)
Templeton's
paper on integration
of evolutionary forces.
Overheads for lecture
20
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 (16 Nov. 2010):
Group
selection, Population structure, Effective population size (Ne), and
shifting
balance
Overheads for lecture21
Lecture22
(18
Nov. 2010): The ecology of speciation
Overheads for lecture22
scanned
overheads
1
of
2 for lecture 22
scanned
overheads
2
of
2 for lecture 22
Lecture23 (23 Nov 2010): Macroevolution
Overheads for lecture23
Jablonski's paper
on macroevolution in gastropods.
Coyne and Orr's paper
on the evolutionary genetics of speciation
Wade's paper on a gene's
eye view of speciation
25 Nov. Thanksgiving.
Lecture
24
(30 Nov 2010). Discussion of
Saetre
et al. Nature: sexually selected character displacement
in a flycatcher. (News
and Views on Saetre et al. paper.)
Discussion
points
for
Saetre
et
al for lecture 22
And possible chalk talk on the evolution of virulence.
-----------------------End of
material for second exam---------------
Lecture(guest)
(2 Dec. 2010) (guest lecture by Prof. L. Delph: genetic collelations)
Overheads. correlated trait evolution
as pdf file.
suggested reading is support of Delph lecture Arnold, 1994
SECOND
EXAM
(7 December 2010)
----------------------Updated
for
2010
above
this
line---------------
Read for Tuesday, December 9th:
Schemske
and Bradshaw PNAS
Lecture24 (9DEC08: Loose ends. Class discussion of
Schemske and Bradshaw)
Lecture 25 (11Dec08): special topic?
C.
M. Lively, Dept. of Biology, Indiana University
Go back to Lively's homepage.