What’s Left in LB145? Last Class: Course Evaluations Take up Exam Begin Evolution Unit Today:
description
Transcript of What’s Left in LB145? Last Class: Course Evaluations Take up Exam Begin Evolution Unit Today:
What’s Left in LB145?Last Class:
– Course Evaluations– Take up Exam– Begin Evolution Unit
Today:– Finish Evolution Unit
Tuesday Apr 23rd:– Bonus survey– Traditional review (?)
Thursday April 25th:– Question-based review (?)
Don’t Forget…
Friday April 19th:View Exams 1, 2, 3 in C4 from 1-3pm. OR Office hours.
Weds/Thurs April 24th/25th:Lab Projects Due.
Friday April 26th: 3-5pm in C-3Last-Gasp Tutorial (email me to reserve a place)
Evolution
Write it Down:What is evolution?
EvolutionWrite it Down:Why is evolution controversial?
Social-Political-Religious Pressures
Source: Gallop Poll 2007
Why is Evolution treated differently from other theories?
1. Social-Political-Religious Pressures
2. It’s presented as belief construct
3. It is complicated and is not often taught/learned very well
Other Academic TheoriesBig Bang Theory, Cell Theory, Germ Theory, Molecular Theory, the Kinetic Theory of Gasses, Molecular Orbital Theory, Variance Bond Theory, Transition State Theory, Marchs Theory, Debye-Huckel Theory, Thermodynamic Theory of Polymer Elasticity, Density Functional Theory, Baeyer Strain Theory, Climate Change Theory, Macroeconomic Theory, Microeconomic Theory, Constructivist Theory, Critical Pedagogy Theory, Multiple Intelligence Theory, Circuit Theory, Control Theory, Systems Theory, Film Theory, Theory of Plate Tectonics, Literary Theory, Approximation Theory, Coding Theory, Intersection Theory, Matrix Theory, Model Theory, Ring Theory, Music Theory, Proof Theory, Theory of Truth, Acoustic Theory, Atomic Theory, Perturbation Theory, Theory of Relativity, Theory of the Mind, Cognitive Dissonance Theory, Attachment Theory, Theory of Self Fulfilling Prophecy, Sociological Theory, Critical Theory, Extreme Value Theory, Performance Theory….
Evolution
Write it Down:How would you explain evolution to a non-scientist?
Evolution through natural selection…
Mouse Fur Color
c(tyr)
Tyrp1Tyrp2p
MC1R protein is stimulated and facilitates cAMP production.cAMP is used to regulate gene expression.
EvolutionEvolution through natural selection…
Pea Seed Taste
Definitions of Evolution…
Evolution – the simplest of definitions:
Evolution – the simplest of definitions:
Descent with modification.
- Nucleotides (mutations!)- Alleles- Genes (deletion/duplication)- Proteins- Cell function- Selectable SPhenotype
Descent with modification of…
Evolution – a diversity definition
Biological evolution is change in the properties of populations of organisms that transcend the lifetime of a single individual. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles within a population to the successive alterations that led from the earliest protoorganism to snails, bees, giraffes, and dandelions.
Douglas J. Futuyma
Evolution is…… the process by which different kinds of living organisms developed and diversified from earlier forms during the history of the earth.
Patterns of Relatedness
Evolution – a populations definition
“Evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next”
Helena Curtis and N. Sue Barnes
Darwin’s Evolution
• Had no knowledge of genetics.• Connected evolution with ecology.
Ecology and Evolution• Beak size in Galapagos Finches
Darwin’s Evolution
?
Darwin’s Finches
Trait Evolution
• The evolution of traits relates to the evolution of species.
Evolution facilitates speciation.
How does speciation occur?
Speciation occurs…
• When two populations become different enough from each other.
Species Concepts• Biological Species – a set of interbreeding populations.• Genetic Species – based on similarity of DNA.• Ecological Species – a set of organisms that occupy the
same niche.• Phylogenetic Species – a group of organisms that share an
ancestor and maintains its integrity through time and space.
• Other:– Typological Species, Cohesion Species, Evolutionary Species,
Morphological Species, Phenetic Species, Recognition Species, Mate-Recognition Species.
Backing Up One Step…What Makes a Species Unique?
One way to look at it:One species can be differentiated from another based on a differing set of traits.
Traits: a functional unit of evolution
• If you can describe how a trait evolved and why a trait is selected for then you can describe evolution.
Evolution of Traits
One More Case:
• Color Vision Evolution in Monkeys
What is colorblindness?
Reduced ability to interpret light as color.
1 in 12 males are colorblind.< 1 in 100 females are colorblind.
Are You Colorblind?
A) No (Female)
B) Yes (Female)
C) No (Male)
D) Yes, very (Male)
E) Yes, somewhat (Male)
Agree or Disagree: It is nearly always advantageous to have trichromatic vision.
(i.e. compared to dichromatic vision)
A. Strongly AgreeB. AgreeC. NeutralD. DisagreeE. Strongly Disagree
Agree or Disagree: Some humans probably have tetrachromatic vision.
A. Strongly AgreeB. AgreeC. NeutralD. DisagreeE. Strongly Disagree
Do you think YOU have tetrachromatic vision?
A. Yes (female)B. No (female)C. I have no ideaD. Yes (male)E. No (male)
Monkeys of the World
NEW WORLDOLD WORLD
TRICHROMATS DICHROMATS
How Does Color Vision Work?Cell Biology:
How Does Color Vision Work?
Three types of Cone Cell
• Different kinds of opsin proteins embedded in the membrane of cone cells.
• Central Dogma of Molecular Biology:DNA RNA ProteinGenes code for…. proteinsProteins are responsible for
cell function
• To produce the signal for color vision, retinal must stimulate the opsin protein but this cannot occur while the retinal molecule is in its cis- formation.
Opsin
Ops
in Im
age
mod
ified
from
Sci
entifi
c Am
eric
an, A
pril
09
3.2a
11-cis-retinal
• When 11-cis-retinal absorbs a photon (a basic unit of light), it changes from 11-cis-retinal to All-trans-retinal.
Ops
in Im
age
mod
ified
from
Sci
entifi
c Am
eric
an, A
pril
09
3.2b
Opsin
11-cis-retinal
Ops
in Im
age
mod
ified
from
Sci
entifi
c Am
eric
an, A
pril
09
3.2c
Opsin
All-trans-retinal
• All-trans-retinal stimulates the opsin in the membrane of the cone cell.
• The cone cell sends a signal to the brain that is interpreted as colored light.
SIGNAL
Ops
in Im
age
mod
ified
from
Sci
entifi
c Am
eric
an, A
pril
09
3.2d
Opsin
All-trans-retinal
The Role of OpsinsThere are three types of opsins:Short Wave Sensitive (SWS)Medium Wave Sensitive (MWS)Long Wave Sensitive (LWS)
An individual who produces only SWS and MWS opsin proteins will have dichromatic vision.
An individual who produces SWS, MWS and LWS opsin proteins will have trichromatic vision.
SWS MWS LWS
3.3
Cone Cell Response to Light
Image from www.answers.com/topic/photopsin
MWS Opsin vs. LWS Opsin
What’s the difference?
Location of Opsin Genes
The gene coding for the SWS opsin protein is located on chromosome #7.
The gene coding for the MWS and LWS opsins are located on the X-chromosome.
Chromosome #7M
Chromosome #7P
Chromosome X1
Chromosome X2
4.2
Origin of the LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.
GENE DUPLICATION
GENE MUTATION
Chromosome X
Chromosome X
Chromosome X
4.3
Gene Duplication4.4
Unequal Crossing Over(Meiosis, Prophase 1)
XMXP XMXPXMXP
Interphase S Prophase I …Telophase II
4.5
Origin of the LWS Opsin Gene
The LWS gene arose through gene duplication and gene mutation of the MWS gene on the X-chromosome.
GENE DUPLICATION
GENE MUTATION
Chromosome X
Chromosome X
Chromosome X
4.3
Chromatic Vision: Opsins
3D Visualization 2D Visualization
The opsin protein is composed of a string of amino acids. Each green dot in the 2D visualization represents one amino acid.
3.4
MWS Opsin vs. LWS Opsinmaqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
MW
S PR
OTE
IN
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
LWS
PRO
TEIN
http://www.ncbi.nlm.nih.gov/genbank/
There are 15 differences between the proteins:
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
MW
S PR
OTE
INLW
S PR
OTE
IN
Seven of these differences results in changes to opsin absorbance capacity.
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
MW
S PR
OTE
INLW
S PR
OTE
IN
Differences at positions 180, 277 and 285 result in an absorbance capacity shift of 31nm.
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
MW
S PR
OTE
INLW
S PR
OTE
IN
What difference does 31nm make?
Positions 116, 230, 233 and 309: smaller absorbance capacity shifts of 1-3nm.
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
MW
S PR
OTE
INLW
S PR
OTE
IN
What difference does 1-3nm make? • Different variants of the MWS and LWS opsins.• Smaller shifts are called “spectral tuning” and can
result in very slight differences in color perception.
Differences at positions 65, 111, 153, 236, 274, 275, 279 & 298 do not cause changes in spectral propertiesmaqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvviasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis vvnqvygyfvlghpmcvleg ytvslcgitg lwslaiiswe rwmvvckpfg nvrfdaklai vgiafswiwaavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccit plsiivlcylqvwlairava kqqkesestq kaekevtrmv vvmvlafcfc wgpyaffacf aaanpgypfhplmaalpaff aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa M
WS
GEN
E
maqqwslqrl agrhpqdsye dstqssifty tnsnstrgpf egpnyhiapr wvyhltsvwmifvvtasvft nglvlaatmk fkklrhplnw ilvnlavadl aetviastis ivnqvsgyfvlghpmcvleg ytvslcgitg lwslaiiswe rwlvvckpfg nvrfdaklai vgiafswiwsavwtappifg wsrywphglk tscgpdvfsg ssypgvqsym ivlmvtccii plaiimlcylqvwlairava kqqkesestq kaekevtrmv vvmifaycvc wgpytffacf aaanpgyafh plmaalpayf aksatiynpv iyvfmnrqfr ncilqlfgkk vddgselssa sktevssvss vspa
LWS
GEN
E4.18
Gene MutationThe LWS opsin is a mutated copy of the MWS opsin. Knowing that most of the difference in spectral sensitivity comes from two differences in amino acid structure of these two opsins), what is the likely number of nucleotide mutations needed for successful mutation from a MWS opsin to a LWS opsin? Position 277: phenylalanine to tyrosinePosition 285: alanine to threonine
Amino Acid Possible CodonsAlanine GCU, GCC, GCA, GCG
Threonine ACU, ACC, ACA, ACG
Phenylalanine UUU, UUC
Tyrosine UAU, UAC
4.19
Can a primate with only TWO functional opsin genes (e.g. SWS & MWS) ever have
trichromatic vision?
A. Yes – definitelyB. Not sure, but possiblyC. No ideaD. Not sure, but probably notE. No – definitely not
- Nucleotides (mutations!)- Alleles- Genes (deletion/duplication)- Proteins- Cell function- Selectable Phenotype
Descent with modification of…
The Ecology ofColor Vision in Monkeys
Food Selection – The Driver of Trichromacy Evolution?
2.5
Food Selection – The Research Part I
F 1,10 = 8, p < 0.05, Smith et al., 2003
TRICHROMATS DICHROMATS
Selected ripe fruit 53% of the time.
Selected ripe fruit 37% of the time.
2.6
Given choice of food…
vs.
Food Selection – The Research Part II
Caine and Mundy, 2000
TRICHROMATS DICHROMATS
Orange-colored Kix
Green-colored Kix
2.7
Food Selection – The Research Part II
Caine and Mundy, 2000
TRICHROMATS DICHROMATS
60% 46%
40% 54%
2.8
Orange-colored Kix
Green-colored Kix
Food Selection – The Research Part II
Caine and Mundy, 2000
TRICHROMATS DICHROMATS
60% 46%
40% 54%Trichromats are more effective than dichromats selecting orange food
in a green environment…
… but dichromats are more effective than trichromats selecting green food in a green environment.
Could there be an advantage to being dichromatic in certain environments?
2.9
Is color vision always an advantage?
• http://www.evo-ed.com/Pages/Primates/PatchGame/PatchGame.html
Food Selection – The Research
Saito et al, 2005
TRICHROMATICVISION
DICHROMATICVISION
2.12
Food Selection – The Research Part III
Saito et al, 2005
The
RESU
LTS
TRICHROMATS DICHROMATS
51% 85%
REWARD
2.13
Recreate this experiment!
Food Selection – Summary
Research suggests that trichromatic
vision is more likely to be
selected for when food is distinguished
from non-food by color.
Research suggests that dichromatic vision is more likely to be selected for when food is distinguished from non-food by shape.
2.14
- Nucleotides (mutations!)- Alleles- Genes (deletion/duplication)- Proteins- Cell function- Selectable Phenotype- And Beyond!
Descent with modification of…
Phylogenetics & Biogeography
1.0
Biogeography of Global Monkeys
NEW WORLDOLD WORLD
FULL COLOR VISION COLOR BLIND
5.1
Hum
an
Chim
panz
ee
Goril
la
Ora
ngut
an
Gibb
on
Rhes
us
Man
gabe
y
Babo
on
Mon
a
Colo
bus
Lang
ur
Woo
ly M
onke
y
Mar
mos
et
Saki
s
Ow
l Mon
key
Squi
rrel
Mon
key
Capu
chin
Spid
er M
onke
y
Color Vision Evolves!Gene Duplication and Mutation
Phylogenetics – Exploring Relationships Among Species
Old World Primates New World Primates
5.3
Geology: Plate Tectonics and Drift
Image: McGraw-Hill Companies Inc.
New/Old World Separated ~ 50 Million Years Ago.
225 million years ago
135 million years ago
65 million years ago
today
5.4
How Old are Primates?
~70-80 Million Years Ago
5.5
When did primates first inhabit North America?
5.6
Hum
an
Chim
panz
ee
Goril
la
Ora
ngut
an
Gibb
on
Rhes
us
Man
gabe
y
Babo
on
Mon
a
Colo
bus
Lang
ur
Woo
ly M
onke
y
Mar
mos
et
Saki
s
Ow
l Mon
key
Squi
rrel
Mon
key
Capu
chin
Spid
er M
onke
y
Continents Split50 Million Years Ago
Color Vision Evolves!Gene Duplication and Mutation
Rise of Primates75 Million Years Ago
Primates In New/Old World55 Million Years Ago
Old World New
World
Monkey Opsins
Exam QuestionHow would you explain evolution to a non-scientist?
- Describe the evolution of a trait from the nucleotide level to the ecological level.
- Nucleotides Amino Acids Protein Cell Function Phenotype Selection Population/Species Level
What’s Left in LB145?Last Class:
– Course Evaluations– Take up Exam– Begin Evolution Unit
Today:– Finish Evolution Unit
Tuesday Apr 23rd:– Bonus survey– Traditional review (?)
Thursday April 25th:– Question-based review (?)
Don’t Forget…
Friday April 19th:View Exams 1, 2, 3 in C4 from 1-3pm. OR Office hours.
Weds/Thurs April 24th/25th:Lab Projects Due.
Friday April 26th: 3-5pm in C-3Last-Gasp Tutorial (email me to reserve a place)