APS125 Population Inheritance Flashcards
What are Mutations?
- Failure to replicate genetic information faithfully
- Can affect the whole chromosome or singlegenes
- Can be spontaneous or induced
- The source of all genetic variation and is necessary fir natural selection and evolution
DEFINITION: Induced Mutation
When the presence of a mutagen increases the rate of mutation
Could be Radiation, UV, X Rays
DEFINTITION: Karyotypes
A method of displaying chromosomes from an organism and numbering them largest t smallest
DEFINITION: Polyploidy
When cells/ nuclei contain more than two sets of homologous chromosomes
In humans its always lethal, eg. after dispermy which results in 3 complete sets
Common in higher plants, bacteria are usually only monoploid with one circular chromosome
DEFINITION: Aneuploidy
When one set of chromosomes is incomplete, eg one is missing or and extra is present
3 types of Aneuploidy in Autosomes
Nullisomy (a pair of homologous chromosomes is missing)
Monosomy (only having a single pair of chromosomes rather than two)
Trisomy (one extra chromosome, usually lethal except during downs syndrome)
Aneuploidy in Sex Chromosomes
If lacking 45X it causes Turners Syndrome, lacking 45Y is inviable
Extra chromosome has minor effect due to X chromosome inactivation
DEFINITION: Translocations
- Exchange of parts between non homologous chromosomes
- Carriers remain unaffected but offspring can have the wrong number of chromosome copies
DEFINITION: Deletions
- Part of the chromosome is missing, patient will therefore only have one copy of the genes in that region
- Severity depends on the size of the missing region
DEFINITION: Inversions
Paracentric- There are two break points in a chromosome and the in-between inverts
Pericentric- The same however the centromere is inside the two breaking points
Types of Coding Region Mutations
- Substitutions
- Insertions/ Deletions
DEFINITION: Substitutions
- Can be silent if base changes but does not change the overall amino acid
- Or Replacement if the base changes the whole amino acid
- Replacement of the middle base will never be silent
DEFINITION: Deletion/ Insertion
- Deletion/ insertion causes a shift which changes the reading frame and produces a different protein
- If entire codon is removed there is less change
DEFINITION: Phenotypic Polymorphisms
Mutation of one nucleotide eg. in Hb beta gene that leads to sickle cell anaemia or what decides the colour of a lizards neck
DEFINITION: Degenerate DNA
- Means DNA can be coded by multiple different codons
DEFINITION: Gametic Mutation
Mutation in sperm/ egg cells
All heritable, can be severe, affects all cells
DEFINITION: Somatic Mutation
Occurs within body cells eg. cancers
Not heritable, usually but not always mild, doesn’t affect all cells
How to cross pollinate peas?
- Anthers removed before pollen is shed
2. Transfer the pollen to other plant by brushing the pollen onto the stigma
What is the ratio for mendelian inheritance?
3:1
Occurred with many different phenotypes in the F2 Progeny
Mendel’s suggestions about Experiment findings
- Alternative versions of a gene causes variation ( Alleles)
- An organism inherits two alleles, one from each parent
- Alleles can be dominant and recessive
- Alleles segregate during gamete production
Mendel’s First Law
Two members of a gene pair segregate from each other during gamete formation, half of the gametes carry one member of the pair and the other from another member
DEFINITION: Particulate Mechanism
Concept that parents pass on discrete heritable units (genes)
Derived from Mendel’s data
How was the first law verified?
- Did a test cross of a heterozygote and homozygote recessive
- Expected equal numbers of purple and white flowers after performing statistical tests
- The data was significant so null hypothesis accepted and the numbers were equal
Dihybrid Crosses
Allow the tracking of two traits simultaneously
Ratio: 9:3:3:1
Mendel’s Second Law
Alleles of different genes segregate independently of each other, ( exceptions when genes are close together)
Known as Independent Assortment
How to verify Mendel’s Second Law
When crossing a homozygote recessive with a Heterozygote observed ration should be 1:1:1:1 which demonstrates independent assortment
DEFINITION: Blending Inheritance
Believed before Mendelian inheritance, however incorrect and would lead to a genetically uniform population
DEFINITION: Mendelian/ Monogenetic Diseases
Human diseases caused by one gene
DEFINITION: Multifactorial Diseases
Diseases caused by a combination of multiply genes
Uses for pedigrees
- Infer modes of inheritance
2. Genetic Counselling, eg risk of offspring inheriting a condition
Pedigree Symbol Definitions
Squares-Male Circles- Female White- Unaffected Black- Affected Diamond- Unknown Sex Black Dot- Carrier Dash- Dead Single Connecting Line- Marriage Double Connecting Line- Inbred Marriage
Autosomal Dominant Disease
- Affected person usually has an affected parent
- Affects both sexes
-Transmitted by either sex - Roughly 50% chance of inheriting
Examples: Widow peak, Polydactyl, Achondroplasia
Autosomal Recessive Disease
- Parents usually carriers/ unaffected
- Effects either sex
- Increased by inbreeding
- Carriers and non carriers are indistinguishable
-If carriers mate there’s 1/4 chance of being affected and 1/2 of being a carrier
Examples: Albinism, Sickle cell anaemia, CF
Cystic Fibrosis
- Most common autosomal recessive disease in Europe
- Affects lungs by increasing mucus production
- Heterozygotes believed to have a selective advantage through resistance to typhoid, cholera
- Caused by inactive copies of the CF transmembrane conductance regulator which is a CL- Channel
X Linked Recessive Disorder
- Mostly affects males
- 0.5 chance of male being affected if mum is carrier
- Females only affected if mum is carrier and dad affected
- Parents unlikely to show symptoms but mothers male relatives might
- Mostly affects males as they’re XY so will always express it
- Impossible for males to pass on to their sons
- E.g Haemophilia
X Linked Dominant Disorder
- Affects either sex
- Offspring of affected female has 50% chance of being affected
- All female children of affected males are affected
- No make children of affected males are affected
Example: Hypophosphatemia
X Chromosome inactivation
- Lyonization
- The inequality of X chromosomes in mammalian male and females is compensated for by X-inactivation
- In each female cell one X is randomly inactivated
- Occurs in early development and all daughter cells will have the same inactivated X
Example: tortoise shell cats
X Linked Disorder
- Only affects Males
- Passed on to all sons but never daughters
- Potentially hairy ear rims
T.H Morgan Fruit Fly Cross A
- F1 Generation all red eyed Females and white eyes males (white is recessive)
- F2 1/4 white eyed males as only have one X which always come from the mother
- Females will always have red eyes
T.H Morgan Fruit Fly Cross B
- F1 white eyed females, red eyed males
- F2 1/4 white males, 1/4 red male, 1/4 white female, 1/4 red female
Why does it matter that genes are on chromosomes?
- There are lots more genes than chromosomes
- Therefore sometimes genes will segregate together on chromosomes, and other times independently
- Its important to see how far apart they are if on the same chromosome
Why might there be some variation in linked chromosomes?
- Recombination occurs where chromatids cross over
- This however is rare and parental types are more common
How to calculate recombination factors?
- Calculate total number of flies/ organisms
- Add the number of observed organism for the two groups you want the distance between
- Divide this by the total
DEFINITION: Additive map distance
When you add together all the recombination factors, not always exactly correct due to double recombinant not always being counted.
To combat this find the square of recombination fraction then subtract from RF
DEFINITION: Loci/ Locus
The physical position of a gene or marker along a chromosome
DEFINITION: Alleles
Different forms of a gene
DEFINITION: Polymorphism
A gene or phenotype with more than one form
DEFINITION: Population Genetics
Studies the frequencies of alleles in a population in order to understand
- forces that determine genetic composition of a population
- the genetic basis, historical background and carrier frequencies of genetic diseases
DEFINITION: Hardy-Weinberg Equilibrium
Allele frequencies in one generation can be used to predict genotype frequencies in the next generation
Hardy-Weinberg Conditions
- Random Mating
- No natural selection
- A large population
- No mutation
Why is Hardy- Weinberg Equilibrium Useful
- Describes how genetic variation is maintained on a mathematic level
- We can detect and question departures, can identify things acting on population genetics
- Useful in medical genetics for carrier frequencies
DEFINITION: Genetic Migration
Introduction of genes from one population to another
How to calculate degrees of freedom
No. genotypes - No. parameters estimated - 1
DEFINITION: Positive Selection
When a gene has two alleles, A1 will have a selective advantage over A2 so overtime A1 will increase in frequency, replacing A2
HIV
- A pathogen causing AIDs
- First recognised in 1981 and now up to 42 million infected
- Single stranded RNA virus
- HIV makes an enzyme called reverse transcriptase
- RT converts RNA into double stranded DNA; key step in HIV lifestyle; prerequisite for replication
3TC Drug Treatment for HIV
- Interferes with normal reverse transcriptase, blocking HIV production
- Some strains have developed resistance
- Mutant RTs have functional defects
- Reverse transcriptase is error prone so HIV has a high mutation rate
- Combination therapy combats this
Sickle Cell Anaemia
- Recessive disorder caused by a mutation in the B haemoglobin
- Carriers develop some resistance to malaria as RBC only become sickly when infected
Balancing Selection
- Heterozygotes are fitter than homozygotes
- Explains why S Allele is kept at high frequencies in malaria infested parts of Africa
Kuru Disease
- Affects the Fore people of Papua New Guinea
- A Prion Disease similar to mad cow disease
- Spread by the consumption of prion infected meat
- Used to take part in cannibalistic rituals which meant this disease spread rapidly
- Higher levels of resistant gene found in older population born before cannibolism was banned
How does habitat destruction affect conservation genetics
- Leads to reduced population sizes which are geographically isolated
- This leads to genetic drift and inbreeding
Genetic Drift
- Loss of genetic variation by chance
- Loss of variation by drift is increased by small populations
- Tend to be less polymorphic
- Alleles drift to fixation and extinction which reduces variation
Elephant Seal Genetic Variation
- Only one population of northern seals survived causing a bottle neck
- N seals had much lower levels of variation than southern seals
Mauritius Kestrel
- 1974 bottleneck where only 4 individuals survived
- Examined genetic markers with micro-satellites
- Could use samples from museums to compare before and after
DEFINITION: Monoculture Effect
Concept that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations
Common issue in agriculture
Wrights inbreeding Coefficient (f)
- Standard measure of the degree of inbreeding of an individual
- Two alleles are identical by descent if they trace their ancestry back to the same ancestral allele
- Calculate the probability that an individual is IBD for locus in question
- 1 being more inbred
Consequences of inbreeding
- Inbreeding depression
- inbred progeny will have higher f values than outcrossed progeny
- Higher frequencies of homozygotes in inbred population
- This reveals recessive disorders and means you’re less likely to benefit from heterozygote advantage
Amish people and Genetics
- Small founder population
- Forbidden to marry outside the community
- Good genealogical records which are used in pedigrees
- High incidence of disorders such as dwarfism, polydactyl
DEFINITION: Multiregional Model
The argument suggesting the transition from H. Erectus to H.Sapiens took place in many places, gene flow between populations
DEFINITION: Out of Africa Model
Less than 200kya H Sapiens emerged in Africa then spread around the globe, replacing other hominids (H. Erectus)
Do Humans have high or low genetic diversity?
- Compared to our nearest relatives we aren’t very diverse
- This supports the Out of Africa Model
Are African Populations more diverse?
- African populations have the most variation at most genetic markers
- Supports out of Africa Model
Out of Africa Evidence
- Humans have low genetic variation
- African populations are most diverse
- Genetic Distance can be calibrated and time of divergence calculated
Two common option for Genetic Markers
- Mitochondrial DNA
2. Y chromosome DNA
Mitochondrial DNA as a genetic marker
- Found in both sexes
- Maternally inherited
- Small molecules
- High mutation rate
- Many copies per cell
Y chromosome DNA as a genetic marker
- Only found in males
- Paternally inherited
- Doesn’t recombine with X chromosome
Genetic markers in Human Population Genetics
- Autosomes can recombine and create brand new genotypes
- TMRCA works best with non recombining molecules
- Used to determine evolutionary relationships between populations, species and sub species
Introduction of Agriculture
- Initiated the switch from hunter gatherer lifestyle to living settlements
- Drove the expansion of the human population
- Infectious disease rose due to living closely together §
Skin Colour adaption
- Determined by melanin
- Bare skin at risk of damage from UV radiation
- This leads to sunburn, sweat gland damage, cancers, nutrient photodegradation
Dark Skin Benefits
- Live in climates with lots of UV rays as protected
- High vitamin D diet means its OK
Light Skin Benefits
- Necessary for Vitamin D production in certain climates, eg Europe
- UV levels are lower
Two types of Melanin
Eumelanin- Black/ Brown
Phaeomelanin- Red/ Yellow
Adaption to diet across the world
Lactose persistence is an adaption
prevalent in European populations where lots of milk in the diet
Adaption to disease
- CF most common autosomal recessive disease in Europe
- Some evidence the heterozygotes are resistant to typhoid
DEFINITION: Discontinuous Variation
- Discrete classes of phenotype
- No intermediates
- Follows mendelian ratios
- Simple genetic basis, limited effect of the environment
E.g Blood Group, pea colour
DEFINITION: Continuous Variation
- Phenotypes don’t fall into classes
- Offspring of intermediate phenotype
- Can’t observe mendelian ratios
- Complex genetic basis plus effect of the environment
E.g Height, blood pressure
DEFINITION: Normal Distribution
- Fully Described by mean and standard deviation
- Variance = SD2
- SD and Variation are measures of spread
DEFINITION: Threshold Variation
- Appears to be like a discontinuous trait, but is continuous
- Distribution called liability
- Phenotype depends on critical threshold
- No simple segregation in families
E.g Diabetes
How do genes influence continuous variation?
- More genes means higher variety of possible outcomes
- There is a relationship between height of brothers but not random people, could be due to same living environment or same alleles
Genetic Twin Studies
- Can compare monozygotic and dizygotic twins
- Both share genes and environments
- Studies on height revealed it is mostly determined by genes
DEFINITION: Phenotypic Variance
A measure of the total variation within a population for phenotype
(Vp)
What are the two components of Phenotypic Variance
- Genetic Variance (Vg) due to different genotypes
2. Environmental Variance (Ve) due to environmental effects
Broad Sense Heritability Equation
Vp = Vg + Ve H2 = Vg / Vp
Why is heritability only a good predictor for short term responses?
- Allele frequencies change over time due to selection/ genetic drift therefore Vg changes over time
- Also environement will change over time
Genotype- Environment Interaction
- Vp = Vg + Ve + Vgxe
- Used to consider quantitatively, called norm of reaction
- Certain genotypes do better or worse in different environments suggesting the presence of an interaction
3 requirements for selection
- Heritable variation
- Competition
- Fitness/ advantage
What limits the reduction of variance when selection is present
- Mutation
- Migration
- Different forms of selection
DEFINITION: Directional Selection
Selection favours an increase in phenotype of interest
DEFINITION: Stabilising Selection
Individuals with intermediate phenotypes are favoured
DEFINITION: Divergent Selection
Favours variants of opposite extremes, leads to speciation
DEFINITION: Frequency dependence
Rare phenotypes might have an advantage, this leads to them becoming more popular and advantage declines
Narrow Sense Heritability
h2
Proportion of variation that can be passed on to the offspring, more useful as concentrates on addictive genetic variance
Broad Sense Heritability
H2
Proportion of variation that is due to differences in genotype, usually more than h2
Narrow Sense Heritability Equation
Change between generations/ Difference between selected group and main group
ie flying speed of drosophila
DEFINITION: Biological Species Concept
Group of individuals that are reproductively isolated from other groups
Reproductive Isolation is a measurable property of the biology of species
Critical Factors for speciation
- A source of divergent selection
2. A source of reproductive isolation
Extrinsic pre mating barriers
E.g different pollinators
Some flowers could hybridise but are pollinated by different species pollinators
Intrinsic pre mating barriers
Different species of crickets have different mating calls so don’t interbreed
Also happens in the lab so no environmental cause
Intrinsic post mating barriers
E.g 2 types of Drosophila Fly
Diverged due to geographical isolation
Unable to mate and produce fertile females or any males
Due to negative epistasis at 2 locus points
Extrinsic post mating barriers
E.g Swainson’s thrushes
2 allopatric subspecies with variable hybrids
However use two different routes for migration to avoid hrs climate
Hybrids take intermediate route with low probability of survival
Effect of geographic overlap on Speciation
A large geographic overlap will have strong homogenising effects of intermixing
A small geographic overlap will reduce gene flow and facilitate emergence
Causes of quick speciation
Allopolyploidy- multiple chromosome sets derived from different species leads to new species
