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Exam 5, Growth Models, Life Tables, HW - Coggle Diagram

- - - - Allele Relative frequency
        
        Number of copies of an allele in a population
        
        Divided by
        
        The total number of all alleles for that gene in a population
        
        What is the brown allele frequency?
        
        30 brown alleles
        
        50 total alleles
        
        So 30/50 = 0.6
        
        What is the black allele frequency?
        
        20 black alleles
        
        50 total alleles
        
        So, 20/50 = 0.4
    - - Number of individuals with a particular genotype in a population divided by the total number of individuals in a population
        
        Genotype Relative Frequency
        
        What is the homozygous dominant genotype frequency?
        
        4 homozygous dominant individuals
        
        25 individuals
        
        So, 4/25 = 0.16
        
        What is the heterozygous genotype frequency?
        
        12 heterozygous individuals
        
        25 individuals
        
        So, 12/25 = 0.48
      - Actual Genotype frequencies
        
        Consider the following
        
        Phenotypes
        
        45 red flowered, homozygous plants
        
        25 red flowered, heterozygous plants
        
        23 white flowered plants
        
        Genotypes
        
        45 RR
        
        25 Rr
        
        23 rr
        
        Actual Genotype Frequencies
        
        Freq of individuals with rr genotype:
        
        individuals homozygous recessive
        
        total # of individuals within population
        
        Freq of individual with RR genotype
        
        individuals homozygous dominant
        
        total # of individuals within population
        
        Freq of individuals with Rr genotype
        
        individuals that are heterozygous
        
        total # of individuals within population
        
        =23/(45+25+23)= 23/93 = 0.25
        
        =45/(45+25+23)= 45/93 = 0.48
        
        =25/(45+25+23)= 25/93 = 0.27
    - - 45 red flowered, homozygous plants
      - 25 red flowered, heterozygous plants
      - 23 white flowered plants
      - 45 RR
      - 25 Rr
      - 23 rr
      - Allele relative frequencies:
        
        Frequency of r: # copies of allele r
        
        Total number of alleles (R & r)
      - Allele relative frequencies:
        
        Frequency of R: # copies of allele R
        
        Total number of alleles (R & r)
  - - - Consider a dimorphic population (2 alleles) such as our red and white flowers with alleles R & r
      - All alleles in the population add up to 100% or 1
      - All genotypes in the population add up to 100% or 1
      - Red & White flower examples
      - Allele frequencies
      - r = 0.38, R = 0.62;
      - 0.38 + 0.62 = 1
      - Genotypic frequencies
      - rr = 0.25, RR = 0.48, Rr = 0.27;
      - 0.25 + 0.48 + 0.27 = 1
    - - Genotypic frequency:
      - RR= 0.38
      - Rr= 0.24+0.24= 0.48
      - rr= 0.14
      - The frequency of gametes carrying a particular allele is equal to the allele frequency for a population in Hardy-Weinberg equilibrium.
      - Multiplying the allele frequencies gives the proportion of each allele combination in the population.
    - - If, instead, we always use p and q rather than choosing an upper and lowercase letter to represent alleles:
      - The frequency of the dominant allele is represented by p
      - The frequency of the recessive allele is represented by q
      - Thus p+q=1
      - Therefore (p+q)2=12;
      - And p2+2pq+q2=1
      - p2= genotypic frequency of RR
      - 2pq= genotypic frequency of Rr
      - q2= genotypic frequency of rr
      - More HW problems
        
        Recall:
        
        23 rr out of n = 93
        
        Allele relative frequencies:
        
        r = q
        
        R = p
        
        EX
        
        Genotypic frequencies
        
        rr= q2=
        
        Rr = 2pq=
        
        RR = p2=
        
        Double check:
        
        p2+2pq+q2=1
    - - Actual frequencies
      - Allele
      - r = 0.38,
      - R = 0.62
      - Genotype
      - rr = 0.25,
      - RR = 0.48,
      - Rr = 0.27
    - - MicroEvolution
        
        Changes in a population’s gene pool from generation to generation
        
        Factors
        
        Mutation
        
        Natural selection
        
        Genetic drift
        
        Migration
        
        Nonrandom mating
      - Mutation
        
        Change in one of the nucleic acids
        
        Some are apparent in phenotype
        
        Source of all new alleles
        
        Must be in gametes to be inherited
        
        Male pollen sperm
        
        Female ovule egg
      - Genetic Drift
        
        Random loss of alleles
        
        Acts most strongly in small populations relative to large
        
        Bottleneck effect
        
        Large population diminished suddenly
        
        Natural catastrophe
        
        Migration
        
        May increase in size again but unlikely to regain original diversity
      - Polymorphism
        
        Dimorphic
        
        2 phenotypes
        
        Dominant-recessive systems
        
        Polymorph = many phenotypes in a population
        
        Example: Aquilegia
        
        Color variation
        
        Spur-length variation
        
        Can be due to a single nucleotide polymorphism
      - Nonrandom mating
        
        Plants “choose” their mates
        
        Pollinator vectors
        
        Pollination syndromes
        
        Some of the individuals reproduce more than others
        
        Based on individual phenotypes
        
        Nonrandom Mating: Sexual Selection
        
        Male-male competition
        
        Excess of pollen grains
        
        Pollen tubes can interfere with one another
        
        Female choice
        
        Barriers on stigma surface preventing germination
      - Migration, Gene flow :
        
        Movement of alleles into and out of a population
        
        Immigration
        
        Into
        
        Emigration
        
        Out of
        
        Can be impeded by
        
        The environment
        
        Life history
        
        Repercussions for
        
        GMO and
        
        climate change
        
        speciation
      - Adaptive radiation
        
        Bottleneck from long distance dispersal
        
        Followed by adaptive radiation
        
        Example: Hawaiian lobeliads
      - Artificial Selection
        
        Selection by humans
        
        Increased frequency of desired trait
        
        Elimination of undesired traits
        
        Crop breeders for thousands of years
        
        Example Brassica
      - Natural Selection
        
        One allele selectively advantageous
        
        In this example, 2 (triangle) has more vigorous offspring
        
        Over time, individuals with the 2 genotype are able to reproduce more and grow in numbers
        
        The overall vigor of the population grows
        
        So does population size
      - Patterns of natural selection
        
        Natural Selection
        
        Steps summarized
        
        Find your Min & Max values
        
        Determine the number of bins
        
        Count the number of observations for each bin
        
        Draw bars for each bin with the frequency
        
        Natural Selection or Not?
        
        Death does not mean natural selection has occurred
        
        Differential survival
        
        Survival due to phenotypes that are heritable
        
        Phenotype coded by genotype
        
        Natural selection related to molecular genetics
        
        Within a population there is allelic variation arising from various factors such as mutations causing differences in DNA sequences
        
        Distinct alleles may encode proteins of differing functions
        
        Some alleles may encode proteins that enhance an individual’s survival or reproductive capacity
        
        Individuals with beneficial alleles are more likely to survive and reproduce
        
        Over the course of many generations, allele frequencies of many different genes may change through natural selection
        
        This significantly alters the characteristics of a species
        
        The net result of natural selection is a population that is better adapted to its environment and/or more successful at reproduction
- - - - Population size (N)
      - Exponential growth
      - J-shaped curve
      - Unlimited resources
      - Logistic growth
      - S-shaped curve
      - Typical of a population that
      - self regulates
      - Has a carrying capacity (K)
    - - r = intrinsic growth rate
      - N = population size
      - K = carrying capacity
      - dN/dt = population change over time
      - Exponential growth
      - dN over dt equals r times N
      - Logistic growth
      - dN over dt equals r times N times the quantity one minus N divided by K
      - Model Details for population growth
        
        Exponential growth
        
        dN/dt = rN
        
        Logistic growth
        
        dN/dt = rN[(K-N)/K] =
        
        rN(1-N/K)
    - - r-selected
      - Grow exponentially
      - Disturbed areas
      - Weedy
      - Annuals
      - Little investment in defense
      - Many, small fruits
      - K-selected
      - Fluctuate around carrying capacity
      - Fairly stable habitats
      - Perennials
      - Invest in defenses
      - Resource-intensive fruits
    - - Plants must make trade-offs due to environmental necessities
      - Many strategies exist
      - Grime’s model
      - Stress
      - Resource availability
      - Water
      - Nutrients
      - Light
      - Growth inhibitors
      - Temperature
      - Toxins
      - Disturbance
      - Biotic
      - Herbivory
      - Pathogens
      - Anthropogenic
      - Abiotic
      - Fire
      - Wind
      - 3 life stages
      - C- competitors
      - S- stress tolerators
      - R- ruderals
  - - - 01April2019 10am: 7,694,293,260
  - - - x = age
      - Nx= number of individuals alive at age x
      - Sx= proportion of individuals of age x that survive to age x+1;
      - Nx+1/Nx
      - lx= proportion of individuals that survive from birth (age 0) to age x;
      - Fx= average number of offspring born to a female while she is age x
      - lx(Fx) = average number of offspring per capita at age x
      - lx(Fx)x = average number of offspring per capita at time x, weighted by age x
    - - Calculate the net reproductive rate (R0)
      - Calculated by taking the sum of the offspring/individual column.
      - Represents the expected number of offspring an individual will produce over its lifetime in the population.
        
        If R0>1, the population size increases.
        
        If R0<1, the population size decreases, and
        
        if R0=1, then population size does not change.
      - Life table practice, G
        
        Calculate the mean generation time (G)
        
        Calculated by taking the sum of the Age-weighted fecundity column and then dividing by the net reproductive rate
        
        Represents average time between two consecutive generations in the lineage of a cohort
        
        The average age between parent and offspring
        
        For humans, typically 20-35 years of age
      - Life table practice, r
        
        Calculate the intrinsic growth rate (r)
        
        Calculated by taking the natural log of the net reproductive rate divided by the mean generation time.
        
        If r>0, the population size increases.
        
        If r<0, the population size decreases, and
        
        if r=1, then population size does not change.
        
        From previous slide
        
        R0=846
        
        G = 1.99
        
        Therefore, r=
        
        ln(846)/G =
        
        6.7/1.99 =
        
        3.39
    - - How long did individuals survive
      - Visual representation of survivorship
      - Type I, typical of K-selected species
      - Type III, typical of r-selected species
      - Dependent on environment
      - Same species can display all 3
    - - Survivorship curves are plotted logarithmically
      - Take survivorship (lx) and multiply by 1000
      - Take the log10 of this value
      - Plot against age to produce a figure
      - Example: Type I curve
  - - - a group of actually or potentially interacting species living in the same location.
      - bound together by a shared environment and a network of influence each species has on the other.
      - factors affecting interactions include
      - abiotic environment
      - biotic interactions that occur between species
    - - Range of interactions
      - Beneficial interactions +
      - Negative interaction -
      - Facilitation (+/+)
      - Benefits both
      - Mutualism
      - Pollination
      - Commensalism (0/+)
      - Benefits one, neutral to the other
      - Amensalism (0/-)
      - Negative to one & neutral to other
      - Competition (-/-)
      - Both are negatively impacted
      - Competition for resources
      - Predation (+/-)
      - Herbivory
      - Parasitism
    - - Predator
      - P
      - Negative impact on prey
      - Positively impacted by prey
      - Prey
      - N
      - Positive impact on predator
      - Negatively impacted by predator
      - Population sizes are influenced by each other
    - - r = intrinsic growth rate
      - N = population size
      - K = carrying capacity
      - dN/dt = population change over time
      - Exponential growth
      - Logistic growth
      - Can similar model predator-prey growth and the impact each has on the other
    - - At low prey and predator population sizes, prey increase exponentially
      - As more food for predators is available, predator survival and reproductive success increases, resulting in predator population growth following that of their prey
      - As predator populations increase, prey death rate exceeds birth rate, resulting in prey decline
      - As prey number declines, there is not enough food to sustain a high predator population and thus predator death rate exceeds that of birth rate
    - - dN/dt = rN-aNP
      - dN/dt=rate of change with time of the prey population
      - r=intrinsic rate of increase for prey
      - N=number of prey individuals
      - a=predator’s per capita attack rate
      - Number of prey eaten per predator per unit time
      - P= number of predator individuals
      - dP/dt = faNP-qP
      - dP/dt= rate of change with time of predator population
      - f=constant, indicating predator’s efficiency at converting the prey it has eaten into new predators
      - q=predator’s per capita mortality rate
    - - Prey population change
      - The number of prey N = 1200,
      - rate of capture or the predation constant a = 0.004,
      - Intrinsic growth rate, r = 0.7 = and
      - Number of predators, P = 130?
      - dN/dt = rN-aNP
      - Predator population change
      - N = 1200,
      - a = 0.004,
      - f = 0.025 predator birth constant,
      - q = 0.12 predator death constant
      - and P = 130 number of predators
      - dP/dt = faNP-qP
- - - - Each chromosome has a partner
      - Homologous chromosomes
      - Resemble each other in size, shape & hereditary information
      - Each homolog is from a different parent
      - Interactions of genes on each sets of chromosomes determines the genetic characteristics
    - - During Metaphase I
      - Orientation of bivalents is random
      - During Metaphase II
      - Orientation of sister chromatids is random
      - In general, the possibilities are 2n
      - Ex: human with 46 chromosomes
      - 246 = 7.04 x 1013
    - - During Prophase I
      - Synaptonemal complex forms
      - Mixes the genes present in homologous chromosomes
      - Results in new combinations not present in the chromosomes of the parental cells
      - Usually at least one chiasma occurs between every pair of homologous chromosomes
    - - New combination of alleles from each parent
      - Promotes heterozygosity
      - Advantages include
      - genetic diversity
      - Bet-hedging to novel environments
      - Multiple deleterious alleles can be bunched together and eliminated
      - Escape host-parasite negative impacts
      - Pollination
      - Cross pollination vs
      - Self pollination
    - - Random placement of bivalents along equatorial plane
        
        Random placement of sister chromatids along equatorial plant.
  - - - Dominance
      - Segregation
      - Independent Assortment
    - - Each individual has a unique genotype
      - Genotype is made up of alleles
      - Phenotypes determined by these alleles (and the environment)
      - There is no guarantee that an allele will manifest
      - Heterozygosity
      - One of 2 genes (dominant allele) has a detectable effect on an organism's appearance
      - The other gene has no discernable effect (recessive allele)
      - Homozygosity, both alleles are the same
    - - Alleles are segregated, separated, from one another during meiosis
      - Each gamete contains only one allele for each gene
      - Offspring inherit 2 alleles for a gene
      - One from each parent
      - Inherit a homologous chromosome
      - During meiosis, 2 members of a gene pair separate from each other
      - Each gamete has an equal chance to inherit either one of the genes
    - - Punnett square
      - Visual representation of the offspring inheritance patterns
      - Monohybrid is a cross between 2 homozygous parents with different alleles.
    - - Gene pairs that are not related (homologs) segregate independently
      - Gene pairs that are not linked segregate independently
      - Evidence provided from a dihybrid cross
      - 3:1 phenotypic ratio for each of the 2 alleles
    - - Same as previous video
      - For reference
      - Parental
      - True breeding
      - Homozygous
      - F1
      - First filial generation
      - Heterozygotes
      - Genotypic ratio
      - Allele combinations
      - Phenotypic ratio
      - Trait combinations
  - - - Phenotype of heterozygote is intermediate between those of parent homozygotes
      - Snapdragons
      - Red x white = pink
    - - Many populations have more than 2 alleles for a particular locus
      - Punnett square theoretical crossing works similar
      - Breeding experiments to determine dominance
      - Figuring out alleles is complex
    - - Changes in the genetic makeup of an individual
      - Point mutation
      - Single nucleotide change
      - Chromosome mutation
      - Deletion
      - Segments of chromosome are lost
      - Duplication
      - Part of the chromosome has doubled
      - Inversion
      - Piece rotates 180
      - Translocation
      - Exchange of parts between 2 nonhomologous chromosomes
      - Transposons
      - Movable genetic element
      - Jumping genes
    - - Fail to mix alleles across homologs
      - Chromosome inherited same as parent
      - Only 2 gamete types possible rather than 4
    - - Multiple genes for one character
      - Phenotype is cumulative result of combined effects of many genes
      - Example abscisic acid
      - Most traits
      - Continuous variation
      - Populations tend to have normal distribution
    - - One gene interacts with another
      - May interfere or mask
      - Ex: digitalis petal color
      - One gene impacts red intensity
      - d light red
      - D dark red
      - Pigment location
      - w throughout corolla
      - W spots of nectar guide
    - - 4 haploid genotypes
      - Not produced in equal numbers
      - Recombinants less abundant
      - Parentals more abundant
    - - Single gene with multiple effects on the phenotype
      - Inheritance of a single gene which visibly influences several traits
      - Ex: awn of wheat
      - Wheat with awns have greater yield than those without awns
    - - Selfer
      - Small petals
      - Flower early
      - Seasonal drought
      - Physiologically escape?
      - Outcrosser
      - Large petals
      - Flower late
      - Seasonal drought
      - Physiologically tolerant?
    - - Having more than two copies (2n) of a chromosome
      - Autopolyploid
      - Failed meiosis
      - Self fertilization
      - Allopolyploid
      - Meiotic error
      - Mismatch during mating
      - Second mating creates matched pairs
      - Polyploidy Examples
        
        Wheat
        
        Result of sequential hybrid doubling and quadrupling
        
        Original ancestral species had 14 chromosomes
        
        Durum wheat
        
        28 chromosome
        
        Tetraploid
        
        pasta
        
        Bread wheat
        
        42 chromosome
        
        Hexaploid
        
        Gluten for lofty bread
        
        Polyploidy Examples
        
        Strawberry
        
        Chemically induced
        
        Prevent microtubule formation
        
        Required for meiosis to occur properly
        
        Produce diploid gametes
        
        During fertilization 2 diploid gametes fuse
        
        Results in tetraploid (4n)
    - - Polyploid mask deleterious recessive alleles
      - Relax selection pressure
      - Accumulate mutations that eventually result in beneficial trait
      - 2 groups of ancient duplications
      - Common ancestor of seed plants
      - Common ancestor of extant angiosperms