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Is the variation in gene expression genetically based?
99% DNA sequence similarity
Fundulus heteroclitus
Evan D’Alessandro
Marine Molecular Evolutionary Genomics
- Evolution
- Ecology
- Molecular Biology
- Genomics
- Genetics
- Population Genetics
- Marine Biology
Future MarineMolecular
EvolutionaryGenomicist?
Charles Darwinb.2/12/1809 (Shrewsbury, England)
d.4/19/1882
The HMS Beagle
Voyage of the Beagle
Two Books Aboard
video
HERESY
DISHONOR
SECRET NOTEBOOKS
Key Question Darwin had:
• Why would life branch out into a tree?
From reading Malthus, Darwin understood:
1- All species struggle
2- All species compete for existence
First Key Idea
Darwin theorized that it would be beneficial under the circumstances of competition and struggle to have more “favourable variations that would tend to be preserved…” and to not have “unfavourable ones to be destroyed.”– Charles Darwin autobiography, 1876
Competition
Winners Losers
SURVIVE DIE
KEY IDEA #2: COMPETITION DRIVES SPECIES VARIATION
1858
• Darwin presents his work (finally!) to the Linean society
• First public airing of his idea that species change and that Natural Selection is a force
• Officially published his idea as a paper on Evolution in 1858
1859
• Darwin publishes ‘The Origin of Species’
• Amazing book
• A masterpiece of arguments for and against evolution
• Evidence and argument
• 2 Major ideas from ‘The Origin of Species’
IDEA 1
Descent with Modification– “From so simple a beginning endless forms most
beautiful and most wonderful have been, and are being, evolved.”
– “Several classes of facts …seem to me to proclaim so plainly, that the innumerable species, genera, and families of organic beings, with which this world is peopled, have all descended, each within its own class or group, from common parents and have all been modified in the course of descent.”
-- The Origin of Species, Chapter 13
“The great tree of life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”
- The Origin of Species, Chapter 4
WHAT DID DARWIN MEAN BY THIS?Break out session
FOSSILS!!
4 Important Fossil Record Sights
1- Burgess ShaleBritish Columbia
2- Dinosaur National MonumentDinosaur, CO
3- Fossil ButteSouth West Wyoming
4- La Brea Tar PitsLos Angeles, CA
Burgess Shale
• Trilobite and Aysheaia Fossils
• Date to 505 million years ago (mya)
• See pg. 308-309 in your text
Dinosaur National Monument
• Jurassic aged deposits
• Date to 150 mya
• Intact full skeletons
Fossil Butte
• Thousands of fish kills found by rail workers in the ‘horizons’
• Palm tree fossil found (tropical climate)
• Dates to 50 mya
La Brea Tar Pits
• Tar served as a preservative
• Hundreds of intact skeletons
• Dates to 38,000 years ago
Key Facts from Fossils
1- Animal and plant forms have changed
2- Timespan of evolution is IMMENSE
3- Extinction is the fate of most species that have ever existed!
4- Environments in every locale have changed, often drastically so…
Fossil Dating• Carbon 14 or 14C- a radioactive isotope• 14C half life is 5,730 years upon which time it turns into
nitrogen 14• Half life- the length of time it takes for half of the
radioactive isotope to change into another stable element
HOW DOES IT WORK?1- Organic matter begins with the same amount of 14C
2- Compare 14C radioactivity of fossil to that of modern sample of organic matter
3- Amount of radiation left can be converted to age of the fossil
4- It’s a ratio!
Earth’s History/Geologial Timescale
Table 18.1 (Chapter 18)
Pangea
We have to understand earth’s history to understand life’s history
Earth’s early atmosphere
• 4.6 bya- earth formed after 10 billion years in the making• Volcanic eruptions (dust)• Inorganic chemicals
– Carbon Dioxide (CO2)– Water vapor (H2O)– Nitrogen (N2)– Hydrogen (H2)– Methane (CH4)– Hydrogen Sulfide (H2S)– Carbon Monoxide (CO)
VERY HOT!
The Earth Cools
- Organic monomers evolved- HOW?
1- monomers came from outer space2- monomers came from rxns. in atmosphere3- monomers came from rxns. at hydrothermal vents
• Proof for outer space- meteorites slamming into earth (bacteria carried to earth)
• Proof for monomers coming from rxns.– Stanley Miller, 1953
• Gases that were thought to be in the earth’s early atmosphere were placed in the apparatus, passed by an energy source (electric spark), and cooled to produce a liquid that could be withdrawn. Chemical analysis found that the liquid contained small organic molecules monomers for large cellular polymers
PRODUCED:Amino AcidsOrganic Acids
Proof for Hydrothermal Vents• NH3 would have been abundant at
hydrothermal vents on ocean floor, not in atmosphere (N2 was in atmosphere)
• Water seeps through vents at 350 deg. F and spews out iron-nickel sulfides which change N2 to NH3
• Lab test confirmed and amino acids form peptides in presence of iron-nickel sulfides
Life’s first Protocell Evolves
• Plasma Membrane- separates the living interior from the nonliving exterior
• Lipid-protein membrane (Sidney Fox)• Coacervate droplets- can absorb and
incorporate substances from the outside solution
• Lipids organize into liposomes (found in 1960s)
• The Cell• See figure 18.4
Lipids from egg yolks placed into water aggregate into microspheres
Nutrition of protocell- simple organic molecules served as food- Took in preformed foods or were chemoautotrophic
(oxidize H2S)- Natural selection favored cells that could extract energy
from carbohydrates to transform ADP ATP
Fermentation
• Lack of O2 in the atmosphere meant that cells had to rely on fermentation for energy
• Glycolysis took millions of years to evolve
DOMAINS
Bacteria– PROKARYOTES
Archaea-- PROKARYOTES
Eukarya-- EUKARYOTES
APPENDIX B- Tree of Life
Prokaryotes– Domains Bacteria and Archaea
• Simple structure• No nucleus
Eukaryotes (protists, plants, fungi, animals)– Domain Eukarya
• Complex cell structure• Nucleus• Organelles, compartmentalized
Protists– Any eukaryote that is not a plant, fungus or animal
SEE FIGURE 4.6 IN YOUR TEXT, CHPT. 4
KINGDOMS
• Domains Bacteria and Archaea are still being categorized
• Domain Eukarya has 4 Kingdoms:1- Protists (ex. algae, protozoans, water molds)
2- Plantae (plants, multicellular photosynthetic)
3- Fungi (molds, mushrooms)
4- Animalia (multicellular, injest and process foods)
Common Ancestor
First CellsBacteria Archaea Eukarya
DomainKingdomPhylumClassOrderFamilyGenusSpecies
EukaryaAnimaliaChordataMammaliaPrimatesHominidaeHomoHomo sapiens
EukaryaPlantaeAnthophytaMonocotyledonesCommelinalesPoaceaeZeaZea mays
HUMAN CORN
BIONOMIAL NOMENCLATURE
Organization of LifeBiosphereEcosystemCommunityPopulation Organism Organ SystemOrgan TissueCell MoleculeAtom
The Last Ice Age
• Also referred to as glacial maximum (18-20,000 years ago)• 13,000 years ago (marked end)• Pleistocene Era• Currently in an interglacial period (Holocene)• Next ice age in approx. 2,000 yrs.
video
The Biosphere
Zone of air, land, and water at the surface of the Earth where organisms exist (Fig. 1.2)
Atmosphere- Air layer
Lithosphere- Rigid, rocky shell of planet
Biosphere- Sum of all ecosystems
Hydrosphere- Combined mass of water
Cryosphere- Portions of solid water on Earth
Anthrosphere- Portion of Earth made or modified by humans for use
What’s in the Biosphere?
Portions of the planet (earth) in which all of life exists, including land, water, and air or atmosphere
Most importantly it contains SPECIES
How does speciation occur?
Reproductive isolating mechanisms
1- Prezygotic- prevent reproductive attempts
ex. Habitat, temporal, behvioral, mechanical, gamete isolation
2- Postzygotic- prevents development
ex. Hybrid zygote mortality, hybrid sterility, F2 (second gen.) poor fitness
Modes of Speciation
Allopatric
Populations separated by a geographic barrier reproductive isolation
Sympatric
Speciation without the presence of a geographic barrier
ex. Autoploidy and Alloploidy (pp. 307)
Biodiversity• Adaptations
– Evolution includes the way in which populations of organisms change over the course of many generations to become more suited to their ever changing environments.
– Diversity is key to species survival
Adaptation for Survival
DECOY
Dots detract from vital organs
CAMOUFLAGE
Predator can’t see
POISONOUS
Alert! Eat me, you die!
Adaptation
How does adaptation drive speciation?Adaptive Radiation
(type of Allopatric speciation)
Ex. Beak of the Finch*Each population adapted to a particular habitat*Different beaks can eat different foods*This leads to speciation, variation and diversity
Darwin’s Key Idea 2• How did all of this variation occur?
NATURAL SELECTION
“Can it then be thought improbable…that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations I call Natural Selection.”
- The Origin of Species, Chapter 4
‘Ingredients’ for Evolution
1- Variation
2- Thousands of generations or TIME
3- Selective advantage
(preservation of favorable traits)
Raw Material + Work + Time = Evolution
Raw Material = Variation
Work= Selection
Generations = Time
=> EVOLUTION
Modern Ex. of Natural Selection and Evolution
Rock Pocket Mouse- Chaetodipus intermedius
video
2 Varieties of Rock Pocket Mice
SANDY DARK
MCIR Gene
How often does a dark coat mutation arise?
DEPENDS ON:
1- Mutation rate
2- Reproductive rate
3- Population size
Mouse Mutation Rate
2 mutations per 109 (ten billion) sites in DNA
10= possible mutation sites in MCIR gene
2 = number of copies of MCIR gene
2 x 10-9 x 10 x 2 = 4 x 10-8
= 1 in 25 million offspring have a dark coat mutation
Is that a long shot?
NO
Why?
Need to account for:
1- Reproduction rate
2- Population size
Rock Pocket Mouse Population
Females (♀) mice have at least 5 babies/yr
Pop. size = 5,000 ♀
SO…5,000 x 5 = 25,000 mice born/yr
25,000 x 1 / 25,000,000 = A DARK MUTATION WILL OCCUR 1 / 1,000 years
YOUR TURN
An American Lobster population size is approximately 50,000 of which 35% are female.
Each female lays 1,000,000 eggs of which only .01% survive
Based on the number of offspring, how long would it take for a blue mutation to spread throughout the population with a total of 5 possible mutation sites, 2 copies of the gene and 1.6 mutations per billion bases?
Hint: Population of offspring times the mutation rate
Calculation
50,000 lobster x .35 (35%) = 17,500 female lobster
1,000,000 eggs x .0001 (.01%) = 100 eggs survive
Total # offspring = 1,750,000
1.6 x 10-9 (lobster genome) x 5 (mutation sites) x 2 (gene copies) = 1.6 x 10-8
1.6 x 10-8 x 1,750,000 = 1/36 years(note- this is just an estimate for this hypothetical lobster population, in real life chances are 1 in 3 million)
How does the dark mutation spread?
1- Depends on population size
2- Depends on the selection coefficient (s)
s- represents the advantage that a dark mouse has over a sandy mouse
s- is a relative measure of fitness and it is a product of reproduction and survival
How long would it take for every mouse to become dark?
If dark mice produce 101 survivors for every 100 mice produced by sandy mice:
This is a 1% advantage s= .01
Over 1,000 generations…
95% of the population will be dark
Video
Natural Selection
SELECTION IS POWERFUL
MUTATIONS ARISE AT RANDOM
SELECTION IS NOT RANDOM!
video
Evolution
Descent with modification/ Variation
Natural selection
Time
Evolution Speciation and Variation in populations
Ecosystems and Populations
An ecosystem consists of the populations of a community that interact among themselves and with the physical enviroment, thereby forming and ecosystem
Populations depend on ecosystems
* Human destruction of ecosystem
How did vertebrates evolve?
Vertebrate Evolution
Text page 541
Common Ancestor
Evolution Continues Today
• YES!!
• Natural selection is still a force acting on human genes resulting in variation
Are we “just the effects of our lucky stars?”
- Stephen J. Gould
The Process of Science
• Observation
• Hypothesis
• Experiments and
Further observations
• Conclusions
• Scientific Theory
• Variation
• Natural Selection
• Fossil Record
Pigeon Breeding
• Variation+NS+ Time
• EVOLUTION
Week 1 Lecture Topics• Basics of life
– Definition, Characteristics and Hierarchy– Ecosystems and Populations– The Scientific Method– Classification and Naming
• Origin and Evolution of Life– Evolution– The Origin of Life– The Geological Time Scale– Cellular History– Kingdoms and Domains
Homework Week 1Chapter 1- ALL
Chapter 2- ALL in preparation for Week 2
Chapter 4- pp 60-61, 68-69
Chapter 15- ALL
Chapter 17- ALL
Chapter 18- ALL
Chapter 29- pp 540-542
Appendix B
Self Tests- Chapters 1, 15, 17, 18
Laboratory Week 1
• The microscope
• Eukaryotic cell staining
