BIOLOGY 1101
SECTION 3004
NAMM 1002
Dr. Cinda P. Scott
cpscott@citytech.cuny.edu
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 Marine
Molecular
Evolutionary
Genomicist?
Charles Darwin
b.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 Shale
British Columbia
2- Dinosaur National Monument
Dinosaur, CO
3- Fossil Butte
South West Wyoming
4- La Brea Tar Pits
Los 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 space
2- monomers came from rxns. in atmosphere
3- 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 Acids
Organic 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 CellsBacteria  Archaea  Eukarya
HUMAN
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Eukarya
Animalia
Chordata
Mammalia
Primates
Hominidae
Homo
Homo sapiens
CORN
Eukarya
Plantae
Anthophyta
Monocotyledones
Commelinales
Poaceae
Zea
Zea mays
BIONOMIAL NOMENCLATURE
Organization of Life
Biosphere
Ecosystem
Community
Population
Organism
Organ System
Organ
Tissue
Cell
Molecule
Atom
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)
• Adaptations
Biodiversity
– 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
CAMOUFLAGE
POISONOUS
Dots detract from vital organs
Predator can’t see
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
MCIR Gene
DARK
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
Common Ancestor
Text page 541
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 1
Chapter 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