Test 4: Genetic Engineering, Population Genetics, Quantitative, Micro and Macroevolution Flashcards
Recombinant DNA technology
- Recombining DNA segments from different species in the test tube
- Reintroducing it back into a living organism
2 Discoveries that made Recombinant DNA technology possible
1) plasmids
2) restriction endonucleases
Plasmids
- bacterial extrachromosomal DNA
- small circular DNA molecules w/ around 2700 bps
Restriction endonucleases
- naturally-occuring enzymes in bactera
- a defense mechanism against invading virus DNA
- bacteria with these enzymes were able to restrict infection
Difference between Endonuclease & Exonuclease
Endonuclease: breaks an internal phosphodiester linkage, fragmentation of the DNA molecule
Exonuclease: breaks the terminal phosphodiester linkage again and again
E.Coli RNA polymerase
- recognizes and binds the promoter to initiate transcription
- does not recognize or initiate transcription at the promoter from another species
Type I diabetes (juvenile onset)
cause: lack of insulin (a protein hormone)
original treatment: bovine or porcine insulin
problem: allergies, side-effects to animal protein
recombinant source: engineered bacterial cells harboring the human insulin gene grown in bioreactors
Dwarfism
cause: lack of growth hormone (a protein)
original treatment: human GH isolated from pituitary glands of cadavers
problem: possible co-isolation of infectious agent
recombinant source: engineered bacterial cells harboring the human GH gene grown in bioreactors
Hemophilia
cause: lack of clotting factor VIII (a protein
original treatment: human factor VIII isolated from donated blood
problem: possible co-isolation of HIV
recombinant source: engineered mammalian cells harboring the human GH gene grown in tissue culture
Genetic Engineering in Plants
- does not usually involve the simple modification of a zygote
- scientists employed the help of bacteria that practice recombinant DNA technology
CRISPR-Cas9 components
- dCas9
- sgRNA 1
- sgRNA 2
- donor DNA
HDR
- homology directed repair (HDR)
- if ligase repairs before HDR, paired nickases will act again
BT toxin
-protein that kills lepidopterans
-extremely species specific: onlu Lepidopterans (moths, caterpillars, butterflies)
-create genetically modified crop plants that harbor
the BT-toxin gene
Why was SCIDS chosen?
1) single gene trait
2) no complex regulation
3) human gene had been isolated and cloned
4) affected organ system easily accessible to genetic modification
Population
- A group of interbreeding individuals
- same species, same range = matings produce fertile offspring
Hardy-Weinberg Equilibrium
- p2 + 2pq +q2= 1
- if =1, in Hardy-Weinberg Equilibrium and allele frequencies will stay the same generation to generation
Polymorphisms
-Many forms (of a trait) in the population
2 Ways for a restriction fragment to differ in length between two chromosomes
1) missing or extra RE recognition site
2) more or less DNA between RE recognition sites
VNTRs
(1/2)n(n+1)
n= number of alleles in the population
Quantitative trait inheritance
-continuous variation between extremes in phenotype
Quantitative traits
-are polygenic (controlled by two or more genes)
number of phenotypic classes = 2n+1 (n = number of genes)
Sample mean
X = sigma(Xi)/n
Xi = each value n = number of values in sample
Sample variance
s^2 = sigma(Xi - X)^2/(n-1)
-need to know X first (sample mean)
establish purebreeding line with smallest value…
… homozygous noncontributing alleles at all genes
establish purebreeding line with largest value…
… homozygous contributing alleles at all genes
Heritability
[S^2(F2) - S^2(parental)]/(S^2(F2)
F1
X = 65 s^2 = 4 s = 2
F2
X = 65 s^2 = 25 s = 5
Determine environmental s^2, genotypic s^2, and total s^2, then determine heritability
environmental s^2 = 4
total s^2 = 25
genotypic s^2 = 21
21/25 = 0.84 heritability
Darwin’s Postulates
1) Individuals within species are variable (VARIABLE)
2) Some of these variations are passed on to offspring (HEREDITY)
3) In every generation, more offspring are produced than can survive
4) Survival and reproduction are not random: The individuals that survive and go on to reproduce, or who reproduce the most, are those with variations that fir the environment best. They are naturally selected. (SELECTION)
Microevolution
-Allele frequency changes in populations (small incremental changes)
Macroevolution
- speciation
- large differences as a result of accumulated microevolutionary changes over time
Allele frequencies will stay the same to generation if… (Hardy-Weinberg Requirements)
1) mating is random
2) no migration
3) no mutation
4) infinite population size (no sampling error)
5) no selection
Nonrandom mating
-Also called assortative mating
positive - like with like (inbreeding)
negative - unlike with unlike (outbreeding)
phenotypic or genotypic
complete or partial
Inbreeding decreases…
Inbreeding increases…
Outbreeding increases…
Outbreeding decreases…
heterozygosity
homozygosity
heterozygosity
homozygosity
Inbreeding coefficient (F)
F = 1 - (observed frequency of heterozygotes / expected frequency of heterozygotes if HWE)
F = 1 - (Het0/2pq)
-if F > 0 = inbreeding
if F < 0 = outbreeding
F will be 0 = HWE
Migration
p(new) = mp(migrant) + (1 - m)p(native)
m = migration rate (fraction of new population composed of migrants)
300 butterflies from the continent are swept to an island where there were 1200 butterflies. The value of p on the continent is 0.4 and the value of p on the island was 0.6. What is the value of p after admixture?
p(new) = (300/1500)0.4 + (1-300/1500)0.6
= 0.56
Migration can change allele frequencies, but does not lead to _________
-adaptations
- but it can affect:
1) direction of allele frequency change, therefore direction of evolution
Mutation
p(n) = p(0) * e^(-nu)
-pn is the frequency of the allele after n generations
n is generations
-p0 is the frequency of the allele now
-e is the base of the natural log
-u is the mutation rate in alleles (gametes) per generation
Mutation alone does not have a significant effect on allele frequencies, but it is the source of new ____
-alleles
Random genetic drift
- an allele’s frequency is free to drift over many generations
- the amount of drift is a function of population size
- does not lead to adaptations
Population size
- random chance events applied to reproduction
- the expected is determined by what he frequency was in the previous generation
Founder Effect
- A population size effect
- small sample of large population founds a new population
- small sample may not reflect the same allele frequencies as larger population
Selection
- differential reproductive success
- not all phenotypes have the same nummber of offspring
- is a function of the environment
Fitness
-selection’s relationship to the environment
1) probability of survival
2) rate of reproduction
Types of Selection
1) zygotic selection - survival
2) sexual selection - finding a mate
3) fecundity selection - gamete production
4) gametic selection - gamete quality
Fitness (w)
w = 1 - s
-where s is the selection coefficient (fraction by which fitness is reduced relative to the phenotype with: maximum probability of survival and maximum rate of reproduction
Direction selection
AA Aa aa
1 1 1 - s
-one homozygote has the highest fitness, other homozygote has lowest fitness
Heterozygote advantage
AA Aa aa
1-s 1 1-s
-heterozygote has the highest fitness
Homozygote advantage
AA Aa aa
1 1-s 1
1 1-s 1-s
-heterozygote has the lowest fitness
Steps of speciation
1) elimination or reduction in gene flow (1 pop becomes 2)
2) Divergence (microevolution + other factors until…)
3) Separate species
Biological Species Concept (BSC)
-If two individuals (from separate intermating populations) mate and produce fertile offspring, they are considered same species otherwise, they are separate species
1) Elimination or reduction in gene flow: Allopatric speciation
- different range
- pop 1 and pop 2 are separated by geographical barrier
1) Dispersal - population migrates to island
2) vicariance - continent separates into island and creates new pop on island
1) Elimination or reduction in gene flow: Sympatric speciation
-same range
-ex: Hawthorn trees are native to North America
Apple trees introduced to NA 350 years ago
some Hawthorn maggot flies began mating on apple fruit
2 populations in the same range mate different times of year apple vs Hawthorn fruit ripening time
1) Elimination or reduction in gene flow: Parapatric speciation
-nearby range (overlapping)
2) Divergence by microevolution: mutation
- same mutations do not occur in both populations
- different alleles appear in each population independently
2) Divergence by microevolution: selection
- if environment is different:
- different selection pressures occur
- under directional selection pattern different alleles become fixed or lost
2) Divergence by microevolution: drift
-different alleles fixed or lost in each population
2) Divergence by microevolution: migration
- both populations are not affected to the same degree
- different alleles fixed or lost
2) Divergence by microevolution: nonrandom mating
-reinforces isolation, and decreases gene flow further
Divergence Microevolution Summary
- Microevolution does not just change allele frequencies
- Over time, alleles can either become fixed, lost or created
- Genetic distance between two different populations increases with time
Inversions
- inversion heterozygotes have reduced fertility (fecundity selection)
- inversion is passed on to half the viable offspring
-inversion gamete + inversion gamete = inversion homozygote
no loop at meiosis, no reduced fertility
Translocations
-translocation heterozygotes reduced fertility regardless of CO events and pass on translocation to progeny
Polyploidy
-instant speciation
Social biology: Cooperative, Selfish, Altruistic, Spiteful
Cooperative: actor + recipient benefit
Spiteful: actor + recipient harmed
Altruistic: actor harmed, recipient benefits
Selfish: actor benefits, recipient harmed
Coefficient of relatedness
- r
- fraction of alleles shared by a relative
- or probability of finding the same allele at any given gene in a relative
r for full-siblings
r = 1/2
r for cousins
r = 1/8
r for aunt or uncle
r = 1/4
Hamilton’s Rule
- if Br - C > 0 then alleles that cause altruistic behavior will increase in frequency by natural selection
- B = benefit (increase in fitness to relative)
- C = cost (decrease in fitness to actor)
- r = coefficient of relatedness
- same as Br > C
Kin selection in Belding’s Ground Squirrels
-Pairie dogs will be more likely to undergo altruistic behavior (warning call) when they have kin at home or offspring
Kin selection in Hymenoptera
- females are diploid, males are haploid (haplodiploidy)
- siblings r = 3/4, progeny r = 1/2
Reciprocal altruism
-natural selection will favor alleles that cause altruistic (fitness decreasing) acts to nonkin if equally valuable (fitness increasing) acts are returned
Prisoner’s Dilemma
- T = 5 points you defect, opponent cooperates
- R = 3 points both cooperate
- P = 1 point both defect
- S = 0 points you cooperate, opponent defects
- T > R > P > S
- R > (S + T)/2
TFT
- tit for tat
- start by cooperating
- repeat opponents last decision
- never defects first
- immediately retaliates for defection
- does not hold a grudge
ESS
- evolutionarily stable strategy
- a behavior strategy is evolutionary stable if:
- population of individuals practicing it cannot be exploited by a rare form practicing another strategy
