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

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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

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3.2b

Opsin

11-cis-retinal

Ops

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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

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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


MW

S PR

OTE

INLW

S PR

OTE

IN

Seven of these differences results in changes to opsin absorbance capacity.



MW

S PR

OTE

INLW

S PR

OTE

IN

Differences at positions 180, 277 and 285 result in an absorbance capacity shift of 31nm.



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.



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


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


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


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


Orange-colored Kix

Green-colored Kix

2.7




60% 46%

40% 54%

2.8

Orange-colored Kix

Green-colored Kix




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

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


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!


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

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Woo

ly M

onke

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Mar

mos

et

Saki

s

Ow

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key

Squi

rrel

Mon

key

Capu

chin

Spid

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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



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

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Goril

la

Ora

ngut

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Gibb

on

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Man

gabe

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Babo

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Mon

a

Colo

bus

Lang

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Woo

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onke

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Mar

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Saki

s

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key

Squi

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Mon

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Capu

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Spid

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onke

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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)

what’s left in lb145? last class: course evaluations take up exam begin evolution unit today:

Documents

critical theory

molecular theory

cell theory

attachment theory

approximation theory

sociological theory

marchs theory

coding theory