Class Powerpoint Flashcards
Do linked genes assort independently?
No
At what stage of the cell cycle do linked genes travel together?
meiosis
What are the different notations for crosses with linkage
- AB//ab
-AB —- (over) ab - ++/ab
- AB —- (double horizontal line) ab
How do you determine linkage?
through a test cross (a cross between a heterozygous individual and a homozygous recessive individual –> AaBb x aabb)
What does crossing over lead to? (regards to chromosomes)
- leads to recombination (recombinant chromosomes)
- if crossing over occurs between two normally linked loci, they will sort independently
If crossing over takes place ever in meiosis …
there will be 50% recombinant progeny
What is different about repulsion (trans-configuration) from coupling (cis configuration)?
- focus on genotypes
- phenotypes of the nonrecombinant progeny need not be the same as the parents
What percentage will be recombinant/nonrecombinant when independent assortment takes place
50% nonrecombinant, 50% recombinant
What percentage will be recombinant/nonrecombinant when complete linkage (genes in coupling) takes place
50% nonrecombinant, 50% nonrecombinant
In a testcross, when given the progeny but not the parents what tells you the genotypes of the parents
the progeny that is the highest numbers
1 map unit =
1% recombination frequency
When does a double-crossover event take place?
arise when two separate crossover events take place between two loci
Does a 1% recombination frequency mean that the genes will be linked together or no?
Yes, the genes are more likely to be linked
What type of gametes does a double-crossover produce?
produces ONLY non-recombinant gametes
What is an advantage of a 3-point testcross?
- the order of three genes can be established in a single set of progeny
- more efficient mapping
- more accurate map distances
- double crossovers are detected
What is the requirement of a 3-point testcross?
one parent must be heterozygous at all loci and the other parent must be homozygous recessive at all loci
Steps to determine gene order
Step 1: identify the parental (non-recombinant) progeny - two most numerous phenotypes
Step 2: identify the double crossover progeny - two least numerous phenotypes
Step 3: identify which gene is in the middle - compare phenotypes of double crossover with phenotypes of nonrecombinant progeny, should be alike in two characteristics and differ only in one, characteristic that differs is in the middle
Steps to determine gene distance
MUST KNOW GENE ORDER FIRST
Step 1: identify the single crossover progeny
Step 2: calculate recombination frequency of first crossover event (crossing over between 1st and 2nd gene)
Step 3: calculate recombination frequency of second crossover event (crossing over between 2nd and 3rd gene)
Recombination Frequency equation
= (progeny from first crossover event + double crossover progeny) / total progeny
Modern Approaches to gene distance
- genetic markers
- DNA detection by specific restriction enzymes (RFLPs)
- microsatellites (tandem repeats of DNA)
- single base pairs
Chromosome morphology is classified by what?
the centromere
what are the 4 types of chromosome morphology
submetacentric, metacentric, telocentric, and acrocentric
what is a karotype?
an arrangement of chromosomes
- collected from cells during Metaphase
- arranged according to size
what are the 4 types of chromosome rearrangements?
- duplications
- deletions
- inversions
- translocations
What are the 2 types of duplications?
tandem and displaced
What are the effects of duplications?
- do not typically result in a phenotype
- if they do can be because of unbalanced gene dosage or the creation of a chromosome loop during prophase 1 of meiosis
What are the effects of deletions?
- many deletions are lethal in the homozygous state
- pseudodominance occurs when the dominant wild-type allele in a heterozygous individual is absent due to a deletion
- creates a chromosome loop during prophase 1 of meiosis
What are the effects of inversions?
- do not typically result in a phenotype
- if heterozygous for a paracentric inversion: recombinant gametes nonviable (no centromere)
- if heterozygous for pericentric inversion: gametes formed do not include all genes
What are the 3 types of translocations?
- nonreciprocal translocation
- reciprocal translocation
- Robertsonian translocation
What are the effects of translocations?
- do not typically result in a phenotype
- when they do can be due to abnormal expression due to new location , the location of the chromosome break may disrupt gene function
- creates a cross like structure during prophase 1 of meiosis
What are the causes of aneuploidy?
- deletion of centromere during mitosis or meiosis (spindle microtubules can’t attach)
- Robertson translocation (small chromosome formed may be lost)
- nondisjunction (failure of homologous chromosomes / sister chromatids to separate in meiosis or mitosis)
What are the 4 types of aneuploidy?
- nullisomy
- monosomy
- trisomy
- tetrasomy
What are the effects of aneuploidy?
- in most cases, aneuploidy is lethal. when it isn’t lethal, most occurs in sex-chromosomes
- lethal in autosomes because they do not have dosage compensation
What are examples of aneuploidy?
- trisomy 21 (down syndrome)
- trisomy 18 (Edward’s syndrome)
- trisomy 13 (Patau syndrome)
What are the two types of Trisomy 21 (Down Syndrome)
primary down syndrome and familial down syndrome
What is the difference between primary down syndrome and familial down syndrome?
Primary is caused by nondisjunction during egg formation. Familial is caused by a translocation between chromosomes 14 and 21
What is polyploidy most commonly seen in?
plants, especially flowering plants and grasses
What are the two types of polyploidy?
autopolyploidy and allopolyploidy
How is polyploidy caused?
nondisjunction in mitosis or meiosis
What are the effects of polyploidy?
- triploidy
- even number ploidy
What are features of polyploid organisms?
- increase in cell size
- physically larger plants
- may give rise to new species
What is quantitative genetics?
the analysis of complex traits
Does the environment affect complex traits?
Yes, they can produce a range of possible phenotypes
What are the types of quantitative traits?
- continuous traits
- meristic traits
- threshold traits
What is polygenic inheritance?
- quantitative characteristics controlled by the cumulative effects of many genes
- individually, each gene still follows Mendel’s laws of inheritance
- can still be influenced by environmental factors
What is the multiplication rule?
The probability of two or more independent events taking place together is calculated by multiplying their independent probabilities
What is the addition rule?
The probability of any two or more mutually exclusive events taking place is calculated by adding the probabilities of the individual events
How does a trait become more “continuous”?
the more genes affecting a trait, the more “continuous” the trait becomes
What is a frequency distribution?
a graph that displays the numbers or proportions of different phenotypes present in a group
What does the variance describe?
provides information about how spread out the distribution is
What does the mean describe?
provides information about the center of the distribution
Phenotypic variance (Vp) =
genetic variance (Vg) + environmental variance (Ve) + gene by environment interaction (Vge)
Gene by Environment interaction (Vge)
- occurs when the effect of a gene depends on a specific environment
Genetic Variance (Vg) =
additive variance (Vg) + Dominant genetic variance (Vd) + genetic interaction variance (Vi)
What are the two types of heritability?
broad sense heritability and narrow sense heritability
Broad Sense Heritability (H^2) =
Vg / Vp
Narrow Sense Heritability (h^2) =
Va / Vp
If heritability = 0
not heritable; all differences from the environment
If heritability = 1
completely heritable; all differences from genotype
If differences between parent and offspring are additive, then offspring …
will have an intermediate phenotype relative to the parents
When given a line of best fit, how can you determine the heritability?
heritability = the slope of the line
What are the limitations of heritability?
- heritability does not indicate the degree to which a characteristic is genetically determined
- an individual does not have heritability
- there is no universal heritability for a characteristic
- even when heritability is high, environmental factors play a role
- heritability is population-specific; the same estimate of heritability cannot be applied to separate populations
What are the strengths to QTL mapping?
can be used to ID the genetic basis of complex traits in non-model systems
What are the weaknesses to QTL mapping?
- can only identify linkage groups, not gene identity
- placement of linkage groups unknown
What are the strengths of genome-wide association mapping?
very high resolution
What are the weaknesses of genome-wide association mapping?
require sequenced genomes for lots of individuals = expensive
What is population genetics?
the study of genetic variation within and among populations, and the evolutionary factors that explain this variation
What is genetic rescue?
the introduction of new genetic variation from outside populations
What is gene pool?
the collection of genes wtihin an interbreeding population
How to calculate genotypic frequency
f(AA) = number of AA individuals / N
f(Aa) = number of Aa individuals / N
f(aa) = number of aa individuals / N
n = total number of individuals in the population
What does genotypic frequency describe?
the gene pool of a population
What does the sum of all genotypic frequencies always equal?
it is always equal to 1
How to calculate allelic frequency for a locus with only two alleles (A and a)
p = f(A) = f(AA) + 1/2 f(Aa)
q = f(a) = f(aa) + 1/2 f(Aa)
What are the 5 assumptions of the Hardy-Weinberg Law?
- large population size
- random mating
- no mutation
- no migration
- no natural selection
What happens when the Hardy-Weinberg Assumptions are met?
- reproduction does not alter allelic or genotypic frequencies
- the allelic frequencies determine the genotypic frequencies
p^2
homozygous dominant allele pair frequency (AA)
q^2
homozygous recessive allele pair frequency (aa)
2pq
heterozygous allele frequency (Aa)
What math rule do you use when Hardy-Weinberg is met?
the multiplication rule
What math rule do you use when Hardy-Weinberg is not met?
can use chi square statical analysis to compare observed and expected genotypic frequencies
What are the two factors that primarily cause a response to selection?
- h^2: narrow sense heritability
- how strong selection is
when narrow sense heritability is high …
offspring will resemble parents
when narrow sense heritability is low …
offspring will not resemble parents
when strong selection is high …
only parents with selected trait reproduce
when strong selection is low …
less stringency on selected trait
how to calculate response to selection
R = h^2 x S
S - selection differential
h^2 - narrow sense heritability
how to estimate heritability from response to selection
h^2 = R / S
What are the limits to selection?
- no more genetic heterogeneity
- reached the limits of the selected characteristic
- additional selection opposed by another selected characteristic
Random mating effects …
genotypic frequency
How do mutations effect allelic frequencies?
- depends on mutation rate (how often it happens)
- the frequency of the allele in the population (if rare, amount of change will be small; if large, there will be many copies of that allele to mutate)
- requires large amounts of times
Forward Mutation
- G1 –> G2
- shifts frequencies from p to q
Reverse Mutation
- G2 –> G1
- shifts frequencies from q to p
Effect of migration on genetic variation
- causes the gene pools of different populations to become more similar
- increases genetic variation within populations
Effect of migration on allelic frequencies
- proportional to the amount of migration
- difference in allelic frequencies between populations
What size of population do genetic drifts more likely occur in?
small populations
A decrease in population size may be caused by
- limitations or space, food, other resources over generations
- a drastic and quick reduction in size (bottleneck)
- establishment of a new population by a small number of individuals (founder effect)
Types of selection and their effect on allele frequency
- directional selection
- overdominance
- under dominance
What is molecular evolution?
the area of evolutionary biology that studies evolutionary change at the level of the DNA sequence
What is the molecular clock?
the rate at which a protein evolves is roughly constant over time
What is the nucleotide substitution rate?
the number of nucleotide substitutions per nucleotide site per year
What are the two types of substitutions?
- nonsynonymous substitutions (nucleotide changes in a gene that alter the amino acid sequence of a protein)
- synonymous substitutions (nucleotide changes in a gene that do not alter the amino acid sequence of a protein)
What are the highest rates of nucleotide substitution rate?
synonymous substitutions
Where are rates of nonsynonymous substitutions the lowest?
coding regions of exons
Where are rates of substitution the highest?
nonfunctional DNA, such as pseudogenes
What are gene duplication events?
substrate for the generation of new genes with novel functions
What are pseudogenes?
a segment of DNA that structurally resembles a gene but is not capable of coding for a protein
What are whole genome duplication events?
substrate for the new generation of new genes with novel functions
- type of polyploidy
What are the types of genome evolution?
- gene duplication events
- pseudogene
- whole genome duplication events
- horizontal gene transfer
What is horizontal gene transfer?
the exchange of genetic information between organisms other than parent-to-offspring inheritance
- more common in bacteria/lower eukaryotes
What is the microbiome?
community of microorganisms in the gut
What is a lower diversity of microbiome associated with?
pathological conditions such as IBS
Where are higher rates of microbiome mapped to?
the industrial revolution and urban areas
