Transcript Document

“Nothing makes sense but in the light of
evolution”
--Theodosius Dobzhansky
1. Outline of course
grading
organization
2. Talk about domestication
disease evolution
Grading
Three exams:
Exam 1
30%
Exam 2
30%
Exam 3 (Final)
40%
30%
100 pts
100 pts
10% (comprehensive)
133 pts
100pts 33pts
Grading
There will be multiple choice questions ~2/3
There will be problem or short answer questions as the material permits
The average grade on exams is ~ 50
The numerical grade tells you little about the letter grade
Grades will be ‘standardized’ in a way that allows for
differences in test difficulty, etc.
There is always a normal distribution of grades
I standardize the scores using a ‘z-statistic’
Your standardized score will depend on the mean and
(score   )
z score 
sd
the variance of the test scores
The mean grade for this course will be in the C range
Organization of Topics in the Course
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Theory of Adaptation
Speciation
Macroevolution
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Biology 3306: Evolutionary Biology
Spring 2004
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Theory of Adaptation
Speciation
Macroevolution
Dr. Blaine Cole
321 G S&R II
713-743-2679
[email protected]
Office Hours:
Wednesday 1:00-2:00 (right after class)
Thursday 1:30-2:30
Or by appointment
Text: S. Freeman and J. C. Herron, 2004. Evolutionary Analysis, 3rd Ed.
Web Page: http://www.bchs.uh.edu/~biol3306/
Date
1/21
1/26
1/28
2/2
2/4
2/9
2/11
2/16
2/18
2/23
2/25
3/1
3/3
3/8
3/10
3/15-3/17
3/22
3/24
3/29
3/31
4/5
4/7
4/12
4/14
4/19
4/21
4/26
4/28
5/3
5/7
Lecture
Reading
Evolutionary Thinking – Evolution around us
Darwinism and the study of evolution
Genetic Variation and Hardy Weinberg
Population genetics--Natural selection, part 1
Population genetics--Natural selection, part 2
Population genetics–Mutation and Selection
Gene flow and population structure
Genetic Drift
Exam 1
Inbreeding and Non-random Mating
Linkage and Recombination
Sexual Reproduction, Quantitative Variation and Heritability
Selection on Quantitative Traits, pt 1
Selection on Quantitative Traits, pt 2, Correlated Traits
Adaptation
Spring Break
Adaptation, continued
Sexual Selection
Sexual Selection
Exam 2
Kin Selection
Life History Evolution
Life History Evolution
Phylogenetic Reconstruction
Speciation, pt. 1
Speciation, pt. 2
Fossils, Phylogeny and Macroevolution
Macroevolutionary Patterns
Extinction
Chapters 1, 2 and 3
Chapters 1, 2 and 3
Ch. 4, Ch. 5 pp 141-154
Chapter 5
Chapter 5
Chapter 5
Chapter 6
Chapter 6
Final Exam 11 am - 2 pm
Chapter 6
Chapter 7
Ch 7, pp 274-288, Ch 8
Chapter 8
Chapter 8
Chapter 9
Chapter 9
Chapter 10
Chapter 10
Chapter 11
Chapter 12
Chapter 12
Chapter 14
Chapter 15
Chapter 15
Ch 16 pp 636-659, Ch 17
Chapter17
Chapter17
Theory of Adaptation
Biology 3306: Evolutionary Biology
Spring 2004
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Theory of Adaptation
Speciation
Macroevolution
Dr. Blaine Cole
321 G S&R II
713-743-2679
[email protected]
Office Hours:
Wednesday 1:00-2:00 (right after class)
Thursday 1:30-2:30
Or by appointment
Text: S. Freeman and J. C. Herron, 2004. Evolutionary Analysis, 3rd Ed.
Web Page: http://www.bchs.uh.edu/~biol3306/
Date
1/21
1/26
1/28
2/2
2/4
2/9
2/11
2/16
2/18
2/23
2/25
3/1
3/3
3/8
3/10
3/15-3/17
3/22
3/24
3/29
3/31
4/5
4/7
4/12
4/14
4/19
4/21
4/26
4/28
5/3
5/7
Lecture
Reading
Evolutionary Thinking – Evolution around us
Darwinism and the study of evolution
Genetic Variation and Hardy Weinberg
Population genetics--Natural selection, part 1
Population genetics--Natural selection, part 2
Population genetics–Mutation and Selection
Gene flow and population structure
Genetic Drift
Exam 1
Inbreeding and Non-random Mating
Linkage and Recombination
Sexual Reproduction, Quantitative Variation and Heritability
Selection on Quantitative Traits, pt 1
Selection on Quantitative Traits, pt 2, Correlated Traits
Adaptation
Spring Break
Adaptation, continued
Sexual Selection
Sexual Selection
Exam 2
Kin Selection
Life History Evolution
Life History Evolution
Phylogenetic Reconstruction
Speciation, pt. 1
Speciation, pt. 2
Fossils, Phylogeny and Macroevolution
Macroevolutionary Patterns
Extinction
Chapters 1, 2 and 3
Chapters 1, 2 and 3
Ch. 4, Ch. 5 pp 141-154
Chapter 5
Chapter 5
Chapter 5
Chapter 6
Chapter 6
Final Exam 11 am - 2 pm
Chapter 6
Chapter 7
Ch 7, pp 274-288, Ch 8
Chapter 8
Chapter 8
Chapter 9
Chapter 9
Chapter 10
Chapter 10
Chapter 11
Chapter 12
Chapter 12
Chapter 14
Chapter 15
Chapter 15
Ch 16 pp 636-659, Ch 17
Chapter17
Chapter17
Speciation
Biology 3306: Evolutionary Biology
Spring 2004
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Theory of Adaptation
Speciation
Macroevolution
Dr. Blaine Cole
321 G S&R II
713-743-2679
[email protected]
Office Hours:
Wednesday 1:00-2:00 (right after class)
Thursday 1:30-2:30
Or by appointment
Text: S. Freeman and J. C. Herron, 2004. Evolutionary Analysis, 3rd Ed.
Web Page: http://www.bchs.uh.edu/~biol3306/
Date
1/21
1/26
1/28
2/2
2/4
2/9
2/11
2/16
2/18
2/23
2/25
3/1
3/3
3/8
3/10
3/15-3/17
3/22
3/24
3/29
3/31
4/5
4/7
4/12
4/14
4/19
4/21
4/26
4/28
5/3
5/7
Lecture
Reading
Evolutionary Thinking – Evolution around us
Darwinism and the study of evolution
Genetic Variation and Hardy Weinberg
Population genetics--Natural selection, part 1
Population genetics--Natural selection, part 2
Population genetics–Mutation and Selection
Gene flow and population structure
Genetic Drift
Exam 1
Inbreeding and Non-random Mating
Linkage and Recombination
Sexual Reproduction, Quantitative Variation and Heritability
Selection on Quantitative Traits, pt 1
Selection on Quantitative Traits, pt 2, Correlated Traits
Adaptation
Spring Break
Adaptation, continued
Sexual Selection
Sexual Selection
Exam 2
Kin Selection
Life History Evolution
Life History Evolution
Phylogenetic Reconstruction
Speciation, pt. 1
Speciation, pt. 2
Fossils, Phylogeny and Macroevolution
Macroevolutionary Patterns
Extinction
Chapters 1, 2 and 3
Chapters 1, 2 and 3
Ch. 4, Ch. 5 pp 141-154
Chapter 5
Chapter 5
Chapter 5
Chapter 6
Chapter 6
Final Exam 11 am - 2 pm
Chapter 6
Chapter 7
Ch 7, pp 274-288, Ch 8
Chapter 8
Chapter 8
Chapter 9
Chapter 9
Chapter 10
Chapter 10
Chapter 11
Chapter 12
Chapter 12
Chapter 14
Chapter 15
Chapter 15
Ch 16 pp 636-659, Ch 17
Chapter17
Chapter17
Macroevolution
Biology 3306: Evolutionary Biology
Spring 2004
Genetic Mechanisms of Evolution
population genetics
quantitative genetics
Theory of Adaptation
Speciation
Macroevolution
Dr. Blaine Cole
321 G S&R II
713-743-2679
[email protected]
Office Hours:
Wednesday 1:00-2:00 (right after class)
Thursday 1:30-2:30
Or by appointment
Text: S. Freeman and J. C. Herron, 2004. Evolutionary Analysis, 3rd Ed.
Web Page: http://www.bchs.uh.edu/~biol3306/
Date
1/21
1/26
1/28
2/2
2/4
2/9
2/11
2/16
2/18
2/23
2/25
3/1
3/3
3/8
3/10
3/15-3/17
3/22
3/24
3/29
3/31
4/5
4/7
4/12
4/14
4/19
4/21
4/26
4/28
5/3
5/7
Lecture
Reading
Evolutionary Thinking – Evolution around us
Darwinism and the study of evolution
Genetic Variation and Hardy Weinberg
Population genetics--Natural selection, part 1
Population genetics--Natural selection, part 2
Population genetics–Mutation and Selection
Gene flow and population structure
Genetic Drift
Exam 1
Inbreeding and Non-random Mating
Linkage and Recombination
Sexual Reproduction, Quantitative Variation and Heritability
Selection on Quantitative Traits, pt 1
Selection on Quantitative Traits, pt 2, Correlated Traits
Adaptation
Spring Break
Adaptation, continued
Sexual Selection
Sexual Selection
Exam 2
Kin Selection
Life History Evolution
Life History Evolution
Phylogenetic Reconstruction
Speciation, pt. 1
Speciation, pt. 2
Fossils, Phylogeny and Macroevolution
Macroevolutionary Patterns
Extinction
Chapters 1, 2 and 3
Chapters 1, 2 and 3
Ch. 4, Ch. 5 pp 141-154
Chapter 5
Chapter 5
Chapter 5
Chapter 6
Chapter 6
Final Exam 11 am - 2 pm
Chapter 6
Chapter 7
Ch 7, pp 274-288, Ch 8
Chapter 8
Chapter 8
Chapter 9
Chapter 9
Chapter 10
Chapter 10
Chapter 11
Chapter 12
Chapter 12
Chapter 14
Chapter 15
Chapter 15
Ch 16 pp 636-659, Ch 17
Chapter17
Chapter17
Domestic dogs are extremely variable
“Domesticated”
from wolves
When were dogs domesticated?
Where were they domesticated?
How many times were they domesticated?
Dogs are the first domesticated species
The oldest remains of true dogs are ~12-14,000 years old
from Eurasia and 9-10,000 from N. America
Phylogeny of dogs
clades
Genetic Evidence for an East Asian Origin of Domestic Dogs
Peter Savolainen, Ya-ping Zhang, Jing Luo, Joakim Lundeberg, and Thomas Leitner
Science Nov 22 2002: 1610-1613.
Coyote
Phylogeny from pre-Columbian dog remains
Latin American
Alaskan
Eurasian Wolves, lu
American Wolves, lu
Modern dogs, D
Humans colonizing America
~12-14,000 years ago brought
dogs with them
Ancient DNA Evidence for Old World Origin of New World Dogs. Jennifer A. Leonard,
Robert K. Wayne, Jane Wheeler, Raúl Valadez, Sonia Guillén, and Carles Vilà
Science Nov 22 2002: 1613-1616.
When were wolves domesticated?
Before 14,000 BP
Where were they domesticated?
East Asia
How many times were they
domesticated?
Once, with occasional
wolf (female) hybrids
What happens during domestication?
1. Animal/plant ‘chosen’ for advantageous traits.
2. Animal/plant deliberately bred for traits.
How do dogs differ from wolves?
Bark
They wag tails
Their tails are curved
Jaw differences
They are hunting ‘companions’
Dogs are highly attuned to the behavior of people
Social cues about the location of food
The Domestication of Social Cognition in Dogs. Brian Hare, Michelle Brown,
Christina Williamson, and Michael Tomasello. Science Nov 22 2002: 1634-1636.
Corn is not so simple
There are variants that occur naturally
The variants can be inherited
Some variants perform better in some environments
Better variants become more common
why should we care about evolution?
-- emergent diseases
-- antibiotic resistance in bacteria
-- pesticide resistance of mosquitoes
1. Transformation of a lineage over time
-- usually short time scale
-- test with experiments or
the comparative method
2. Diversification of one lineage into several
-- often long time scale
-- usually not experimentally tractable
-- phylogeny reconstruction
HIV as an evolutionary case study
Adaptation - how populations change through time
in response to environmental change
(lineage transformation)
-- AZT resistance
-- evolution of lethality
Diversification - how new forms arise
-- origins of HIV
-- evolution of lethality
HIV
retrovirus (RNA)
attacks T cells (immune system)
normal: 800-1000 cells/ml
AIDS:
<200 cells/ml
death by secondary infection b/c immune
system destroyed
destruction of T cells
changes in virus
}
reduce recognition
of virus as foreign
HIV is a retrovirus -- reverse transcriptase
AZT:
azidothymidine vs normal thymidine
= stop codon
is AZT resistance due to infection with a different HIV ?
1. resistant individuals often have the same
change in the reverse transcriptase
2. stopping AZT causes resistance to decline
HIV quickly becomes resistant to drug treatments
Evolution of resistance to AZT
reverse transcriptase errors
non-mutant
mut1
mut2
mut3
mut4
mut5
killed by
AZT
X
slightly
resistant
X
X
X
mut2.2
mut2.3
X
X
nonresistant mut2.1
X
AZT resistance is an example of evolution by
Natural Selection
1. mutations by reverse transcriptase produce
variant HIV molecules
2. mutants are passed to ‘offspring’ of resistant
genotypes
3. differential survival in AZT environment
resistance is costly (slow growth). Mutants
differ in enzyme function
4. resistance becomes typical
effectiveness and speed of process
-- rate of mutation ( ~1%/yr)
-- strength of selection
Influenza
RNA virus
Spreads rapidly
Human immune system
affects flu
Time period 1985-1996
HA1 gene (Hemagglutinin)
Type A subtype H3