Ecology

Lecture #2
Monday, January 27, 2014

9:16 AM

E-mail: Ssukhdeo@aesap.rutgers.edu
• Evolution - inherited changed over time.
1.) Inherited --> talking about something that is passed down into the next generation => offspring.

DNA

…..CCTTAAGG…..
…..GGAATTCC……..
3 Billion pairs

DNA = Deoxyribo nucleic Acid
4 building blocks
Cytosine = C

A-T;C-G

Thymihe = H
Adenine = A
Gnanine = G
1.) Genes - Discrete hereditary unit composed of specific nucleotide sequence in
DNA
- Evolution - must be able to pass on (Genes) to be considered
2.) Change --> Variations in the actual gene or DNA sequence
--> Mutations: CCTTTA
GGAAAT
CCTTAA
GGAATT
Mutations are not always bad. (DNA allows for small mistakes)
3.) Time --> Long time millions and millions of years (most people think that)
But No --> it can be only past just several generations
- Species: Individual that have the potential to interbreed and produce a "live, viable, fertile young."

Middle Ages (5th - 14th Century)
- People organized everything into the "ladder of life"
- Aristotle "Scala Naturae"
- God is top of the ladder , Humans second ….. Tea cup & slimy animals
- No extinction --> all animals and plants on Earth has always been there and will continue to be there. What they saw was always on earth, will always be on earth. SO NO DINASOURS.

Early 1800s
- Georges Cuvier ---> Found fossils: bone, tooth, jaw
- Most scientist believed that all living things were immutable
○ Latin - unchanged
1822 -** Gideon and Maryann Mantell in England
- Spent years digging it out and found the first complete fossil
○ Of an Iguanodon

Christian Scientist - said they must be "Antediluvian" "Dinasour"
Ante (latin) = before
Diluvian (Latin) = the deluge (Flood)

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Lecture # 2.2
Monday, January 27, 2014

9:57 AM

So Christian Scientist believed that the animals were too big to fit into the arc and so they all drowned.
Charles Darwin (1809 - 1882)
- All of his family was successful Doctor: but he is a failed medical student
- So became a theologist
- He was a naturalist:
○ Collecting
○ Dissecting
○ Hunter
○ Pigeon Breeder (understood things were being inherited)
○ Knew about animals and plants
○ Became friends with all the naturalist, zoologists, botanists (plants).
- HMS Beagle (Ship that Darwin got on)
○ Captain Robert Fritzroy (also a naturalist, but famous only because Darwin was on his ship)
 Survey coastline of South America. 2years trip. --> but lasted 5 years.
□ Darwin collected, collected and wrote down details about everything, collected plants and information.
 Galapagos Island (600 miles West of Ecuador)
□ Volcanic islands (like hawaii!)
□ Darwin stayed on that island for 27 days
Galapagos Island (Galapagos --> "Saddle")
1.) All animals were very tame --> implied that there were very little human contact.
2.) many animals and plants were Unique to an island
3.) Butt --> even if animals + plants were unique
Resemble animals + plants looked mainland SA.
Did not resemble animals plants in England & Europe
- Went home and waited 22 years
○ How animals + plants get on island? --> blow off course

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Lecture #3
Thursday, January 30, 2014

9:13 AM

• Waited 22 years to write his book (don’t need to know numbers)
○ Gets manuscript from Alfred Wallace, he worked on SE Asia Islands. He was a entomologist --> study of insect
 Malay Archipalago. He observed that species were unique on the island. And similar species were the same as nearby islands.
 Created the "Wallace's line" on the bottom side of the line, animals were from
Australia. Top of line, aniamlas were from China
□ Continental drift - lands drifting apart

○ 1859 Charles Darwin wrote the book
 " The origin of species by means of natural selection o the preservation of favored races in the struggle of life". His entire book name.
○ Alfred Wallace Book
 " On the tendency of varieties to depart indefinitely from the original type"
 Darwin --> Competition for resources
 Wallace --> Adaptation
○ Long paragraph by Darwin - Theory of Natural Selection
 Why didn’t he use "Evolution" ?
○ Latin = evolutio = unrolling of a scroll
 Linear
 Predicted
 Ordered
 But Darwin did not want to use this word b/c it's not predicted and not ordered.
 Quote = 4 important points
 1.) More offspring are born than survive
□ It is a competition/ struggle. Adullthood + reproduce
 2.) Environmental resources are ALWAYS limited (finite). Eventually resources will run out. □ Resources: Food, Water, Oxygen, Space, Soil nutrients, sunlight, shelter, mates.
 3.) Individuals of a species are variable
□ Phenotype --> expressed variations (different hair color, different nose). Have to have variation because you don’t know what's going to happen in the future. (e.g
Disease will kill off everything)
 4.) Variations must be able to be passed onto the next generation --> Inheritance.
○ Natural Selection - Differential (Unequal) survival + reproduction of individuals with certain advantageous traits will contribute disproportionately to the makeup to the offspring in the next generation.  Advantageous traits that are unpredicted/unknown. But we hope that we have such a wide variety of genes, that we hope our genes will survive.
 Population: all individuals of a species living together in the same time + space
 Natural Selection - Adapting to the local environment
 Gene diversity (variation).
○ Darwin's finches - birds that all have different beaks on the island were different in his country. Darwin find that the beaks have to adapt to find food.

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Lecture #4
Thursday, February 06, 2014

9:25 AM

"Survival of the fittest"
- Fitness = contribution an individual makes towards the next (future) generations relative to other individuals of the same species.
- Your contribution to the gene pool (that’s "fitness")
- Grandparents are most fit if they can pass on their genes down 2 generations
- Adaptation to the local environment
3 examples of natural selection
1.) Peppered moths in England (Hunt at night, daytime they hangout in trees).
- Predator of moth --> birds
 2 color variants --> whiteish peppery , Dark brown with spots
 Lichen tree--> fungi + phtsythietic algae, lightish mottled color
 Scenario 1 - Pre industrial revolution pre 1800s England.
□ Lichen is whitish colored. More likely the whitish moth will survive.
 Scenario 2 - Full industrial revolution -- buying coal, wool
□ Lichen is white but air particles turn the tree with air pollution turns dark. Darkish moths will survive more than whiter.
 Adapted into the local environment
 Scenario 3 - After Industrial revolution cleanup. Whitish has more than darkish 2.) Deer Mouse - Peromyscus Maniculatus
- South hills, Nebraska
- Mixture of prairie grass and sand dunes (quartz and grain sand)
- Deer mouse -> 2 color dorsal coat variant
 In the Pairie grass area -> found more dark brown in coats mouse.
 Sand area --> found more brown/sandy color
 = Pressure --> Predation
□ Found a gene - hair color called: Agouti Gene --> controls melanin production.  This was a mutation that produce sandy colored mice. This occurred 8000 years ago. (sand 1000-1500 years)
 This Agouti gene contains in many species. Cows, deer
 Mouse mutation occurred for 2000-7000 years.
 Blond __ Prairie: BAD, Sand: mixed in/ Advantageous
□ So sandy colored lived more.
3.) Plant - Field mustard, California
- Vary --> Pollination time, Flowery time, fruity time, waiting pollination (bird, butterfly) - CA --> field mustard collect seeds. 1997-2004…
 Drought hit 2000-2004 (blistering sun, little water)
 They want to compare if there is a difference in seeds between pre drought? And after drought?
 Took seeds 1997 + took seeds 2004 and planted in greenhouse. Put the pots all under same condition. 2004 seeds actually mature 8-9 days earlier. Micro evolutionary mechanisms
- Changes in gene/ allele frequencies
- Allele = gene variant
- One allele = mother
- Second allele = father cells
- Egg and sperm half and half makes full.

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Lecture #4.2
Thursday, February 06, 2014

10:13 AM

Mom allele + Dad allele
W white ; w dark
Ww
WW = Dominant
Ww = Whitish ww= dark
Micro-evolutionary mechanism : Changes in gene/ allele frequency.
What changes the alleles frequency?
- Natural Selection
- Mutation (can always change the genes or and the allele
○ Advantageous mutation --> sweep through population.
○ Deleterious mutation -> died off, bad
 E.g. Point mutation --> one nucleotide changed. Sickle cell anemia.  [GAG] - Amino Acid
[CTC] -------> normal cell
 [GTG] - Amino Acid
[CAC] ----> Sickle cell
○ Normal RBC
○ Sickle Cell
 Carry less O2 = resistant malaria
 Joint pairs
 If you live in Sub-sahara aftrica:
○ ShSh --> Normal (will die from malaria)
○ Shsh --> Hetrozygeous (will survive from malaria) but suffer a little bit. It's okay.
○ shsh --> sickle cell anemia (Fatal)

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Lecture #5
Monday, February 10, 2014

9:13 AM

(cont. previous lecture)
Micro evolutionary Mechanisms
- A change in gene/allele frequency within a population
- Population --> evolution / natural selection occurs at this entire population.
4 Ways of evolutionary mechanisms - changes in gene and allele frequency
1.) Natural selection
2.) mutation --> Advantageous (accumulation of all kinds of advantageous genes).
3.) Gene flow - Gain or loss of allele from a population due to movement of individuals. (e.g immigration -- moving INTO a population; Emigration - when you move OUT into a population)
- Many young adults move out.
4.) Genetic drift - random changes in allele frequency in a population.
- 1 important factor: will only see a generic drift in a SMALL population.
- BUT --> genes on cook campus 1964 --> 2014. 2000ppl--> 3000ppl

2 Ways of genetic drift
1.) Bottleneck effect - a disaster strikes and wipes out over 90% of population. --> survivors are pure
LUCK.
- e.g vocano burns everyone in NJ but the people in this class. (only the blue genes will pass, no green or red genes)

- e.g Colonization of North American (this happened before). It was all ice before so the Native
American walked down south to America and colonized. They were the first and original people to colonize America.
○ ABO = Blood group (blood types). A, B, O, AB
 Africa --> 1/3 A, 1/3 B, 1/3 O
□ Ancestor population always has the diverse genes
 Europeans --> all have equal A,B,O
 North & South American Native Population --> 90%-100% have O blood type.
□ The people that crossed to south america, by CHANCE, all these people happen to have blood O type.
○ [EXAMPLE OF GENETIC DRIFT]
2.) Founder Effect - Same result but small population breaks off from a large main population and then interbreed with each other. You'll see genetic drift because of the different environment so humans adapt it. --> eating tree barks, teeth will be harder.
--> some point will become a new species.
e.g Martha's Vineyard (Massachusetts). They voluntarily left and went to Martha's Vineyard. At some points in early 1900s, >80% of people at Martha's Vineyard were deaf

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Lecture #5.2
Monday, February 10, 2014

10:16 AM

Artificial Selection
- Selective breeding of domesticated plants + animals.
- Jean Baptiste Lemarck (1744-1829)
- "Inheritance of a acquired character", only the people who can adapt to the environment can survive. - e.g Giraffe --> ancestor use to look like a deer, now they have long neck. Humans have 7 vertebrates, giraffe has 7 too but WAY BIGGER.

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Lecture #6
Monday, February 17, 2014

9:23 AM

4 ways of microevolutionary mechanism
1.) Natural Selection
2.) Mutation
3.) Gene flow
4.) Genetic drift - accumulation + lot of change. ----> can't breed with the original species. (Reproductive organ structure changed). -------------------> going to start to get a new species
Speciation - divergence of existing species into new species
A (original) --------> B (living)
A (original) --> B
A
A (Original) -->

C
B

2 Ways that can cause Speciation (in addition to mutation, n.s)
1.) Allopatric speciation
Allo (greek) = different
Patric (greek) = country
- A barrier (physical) arises that splits a population into 2 groups that cannot mix back (no gene flow)
- **TEST e.g. Grand Canyon
○ Found 2 species of squirrels --> one on either side of the canyon
(no gene flow)
○ A (isolated) --*eons (many years gone by)--> adapting -----> B
○ B (isolated) --* eons ---> adapting ---> C
- e.g Adaptive radiation (extreme example of allopatric speciation)
○ Species that give rise to multiple specific that explicit different niches (niche = what animal/plant needs to grow)
 Hawaiian island
 Galapagus island
 SE Asia Island

Hawaiian Islands
.> 8000 species of flies (3000 species of snakes worlwide) Ecology n Evolution Page 8

Lecture #6.2
Monday, February 17, 2014

9:46 AM

Hawaiian Island -- Active volcano (flies on the rock survives)
- Species 1, species 2, 3, 4
- Must have : Isolation, no gene flow, reproductive isolation
2 Ways that can cause Speciation (in addition to mutation, n.s)
1.) Allopatric speciation(SEE ABOVE)
Allo (greek) = different
Patric (greek) = country
2.) Sympatric Speciation
Sym (greek) = together
Patric (greek) = country
- No physical barrier
- Speciation without barrier
- African savannah --> multiple species of herbivores (eat plants)
Sympatric speciation
- Easy to see in plants
- Polypoidy = fusion or incomplete separation of chromosomes
Human = 46 chromosomes
--> egg = 23 (1n)
--> sperm = 23 (1n)
Egg + Sperm --> zygote = fertilized egg --> human = 46 (2n)
BUT IF Zygote = 92. Sperm (2n) + Egg (2n) = 4n ----> Polypoidy
- Does not happen in animals (or else we die immediately)
- Happens all the time in plants - main ways a new species develops
Mutation:
e.g. Seedless watermelon = 3n
Wild oats = 2n. Domesticated oats = 6n (there's no barrier in the farm, but just happens, mutations) 1 individual --> very very different
How fast speciation occur? Billion of years? --- generations
What causes speciation? Intense selection pressure ( many selection)
Eg Cockroaches --> florida
Research house - millions of cockroaches
- Cockroaches bait traps
- Bait --> poison --> cockroaches turns to bait --> cockroaches loves sucrose (sugar).
- 5 years ago --> cockroaches were avoiding the bait
○ Now, sugar receptors --> turns from pleasure to disgust
- Drug resistance -> speciation
□ Mutation --> hugely advantageous
□ Happens to bacterial resistance
□ Pesticide resistance

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Lecture #7
Thursday, February 20, 2014

9:00 AM

Evolution of Sexual Selection
- Darwin wrote a book in 1871 "The decent of man and selection in relation to sex"
- Darwin defined as:
The process that depends on the advantage that certain individuals have over other individuals of the same sex + species in exclusive relationship to reproduction.
2 Kinds of selection:
1.) Intrasexual selection
2.) Intersexual Selection
1.) Intrasexual Selection
- Intra (latin) = within
- Individually of sex (usually male) gain competitive edge by fighting with each other.
○ Winners - gets females
○ Losers - gets nothing
○ Male - male competition e.g Lions, bears, elephant, Elk, Gorilla
- Sexual dimorphism = one sex is much larger than the other sex
○ Male > female
 Tusks, horns, claws, fangs, speed, size, aggression, insects, fish, lizards
 Selection Force: Aggression, Big, tough
□ Alpha Male
□ Male + multiple female = Harem
□ Male - Male competition for females (harem)
2.) Intersexual Selection
- Inter (latin): Different sexes
- Selective mate choice
- Individually of the sex in demand (females) choose mate with certain preferred characteristics
○ Female mate choice = looking for --> protection? Odor, smell, money???
- Conflict between male + female --> sperm + egg

Male

Female

- Sperm (very small)
- Produce lots and lots of sperm (produce a lifetime) - --> cheap (small energy investment)
- Have sex with multiple females in breeding season
- No risk of being pregnancy - No paternal care

-

Egg (very huge)
2 hundred egg, limited of eggs
Cannot make it lifetime
Limited time for reproductive
Egg --> lots of energy investment
Female --> mated in a season (DONE)

- Huge risk in pregnancy (predation)
- After birth, huge amount into maternal care

*Huge conflict difference between male vs. female!**

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Lecture #7.2
Thursday, February 20, 2014

9:30 AM

• Female mate choice (always female making the choice)
○ Female gets to pick the male they get to make with.
○ Female looking for? "preferred characteristics"
 Strong, big, colorful, good genes
 Good immune system, good color, good symmetry, good sperm (how do you know?)
 Paternal care
□ Male wants OFFSPRING = Fitness
□ Female selective: male looks for:
□ Female traits: surrogate traits, one physical trait that relates information about another trait that you cannot see/ measure
• Example: 15 -spine stickle back fish (2 inches)
Female
male (red bellies)
Red belly --> comes from eating carotenoid
- Carotenoid food e.g carrot, red leaves, red plants
- Redder the belly --> male eat more carotenoid food.
- Females always choose - redder belly male.
Stickle Fish --> live in a low oxygen environment
- Redder belly male --> fan the eggs move frequently to increase oxygen content over eggs. More eggs hatch + survive.
• Example: Symmetry --> good steady nutrient during development
--> inherited some good genes
--> accident (more risk)
--> lose a fight
Barn Swallow Bird
Female only pick symmetrical tail in male.

This is why males have elaborate color feathers, long beaks, elaborate calls.
---> signal females, risking death by predators.

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Lecture #8
Monday, February 24, 2014

9:00 AM

Midterm - 64 MC questions, 9 Questions each
Experimental Evolution
>10 years --> trying to see if they can see natural selection occuring.
- Went to have animals species that reproduces fast
[has to happen in the lab, b/c can happen very fast]
--> e.g E.Coli = Eshericolio Coli
Humans = homo sapiens
Example: Dr. Richard Lenski - Michigan State
1988 - 12 flasks of E. Coli
Known # of E.Coli
--> single cell bacteria
--> fed them single sourced glucose
1.) Added glucose once a day at some time
2.) every 24 hours --> remove aligout (specific amount) new flask + glucose
24 hours later
E.Coli --> 1 generation takes 3.5 hours
1 day, you'll have 6.6 generation
25 years around = 58,000 generation
After 75 days --> 1% of each flask they freeze it. [has over 4,000 frozen sample]

Experiment 1 - After 2000 generation, he changes the nutrient source. [Normal = sugar (glucose)]
>2000 generation --> maltose (different sugar)
--> Many many flask died. SOME flask very low survived.
--> kept giving maltose, 1,000 generation later…
All of them adapted to maltose.
Experiment 2 - 2003 (15 years after the start)
- Noticed some flask become turgid (cloudy) after 24 hours.
○ Thought it was contamination by something else (another bacteria)
○ So they defrosted a earlier sample --> re started the line from the flask.
 It got cloudy again before 24 hours.
 Over a year testing
 E.Coli --> fed 1 times a day fed glucose --> E.Coli binge eat
 Found some E.Coli have mutation to consumer citrate (acid)
□ Citrate (acid) - part of energy cycle --> in one cell
- Mutation --> cloudy flask were consuming citrate, not glucose
- Gene duplication --> move then 1 copy of specific gene (NOT a gene/allele variation)

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Lecture #8.2
Monday, February 24, 2014

9:30 AM

Experimental 2 cont.

Color

feet size

insanity

aggression
---> Gene duplication

Duplicated citrate transport gene
Gene A = Citrate transport gene is vital for survival
Mutants --> 2 copies
1st copy doing normal work
2nd copy --> free to do something else
Citrate --> food source
2nd copy is extremely advantageous (can process their own nutrients)
- Copy Number Variations (CNV - gene copies)
○ Prediction of disease condition
 Too few too many
Diseased
diseased
- Example: Human epidemal growth factor reciptor
○ ERBBL --> too many copies --> Breast cancer
○ (good example) CCL3L1 --> Too many --> Supress HIV infection
Experiment 3 Mexican Tetra Fish, 2013 December
- Fresh water
- Creeks, river
- Drab Colin
- Many Species
- Some species moved into caves
- Long time ago --> eyeless + no eye socket
- Mutation? Why did it evolve? Is it beneficial?
- Why beneficial in pitch dark cave to have no eyes?
○ Energy spent on developing, maintaining, growing the eye is used for something else.
- What is the mutation?
○ Heat shock protein 90 gene (HSP90)
 Function: make sure other protein are folded properly
 Proteins are 3D structure and made linear - folded
 Stabilizing proteins against heat strokes
 Suppressing tumor formation
 HSP90 --> proteins perfect
- Initial Tetra --> moved into cave
○ No light + water different (less salty)
○ Because conditions were extreme--> HSP 90 Gene was suppressed --> allowed mutation --> becomes eyeless + gained other traits.
In fishes

--> experiment --> suppress HSP90 --> abnormal eyes, legs, other traits

Fruitflies

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