In class notes Flashcards
How many base pairs are in the human genome?
6 billion pairs
What is a synonymous substitution?
nucleotide substitution that don’t cause an amino acid change
What is a non-synonymous substitution?
nucleotide change that causes an amino acid change
What is the rate of synonymous to non-synonymous substitutions indicate
used as an indicator of selection pressure
What is a gene
stretch of dna/rna that is subject to natural selection
what is an allele
a variant of a gene
what is a locus
place where you find a gene in a genome
What is a genotype
diploid contingent of alleles
what is my haplotype
haploid contingent of alleles
what is a phenotype
- expression of genotype
- what your genotype codes for
- things that selection can act on
what is a snp
- single nucleotide polymorphism
- a variation at a single position in a dna sequence among individuals
Do SNPs occur normally throughout an individuals DNA
- yes, most have no effect on health or development
- when they take place in a gene or near it in the regulatory region they can have negative effects on gene
What is biological evolution
changes in gene frequency over generations
what does biological evolution lead to
descent with modification
what is descent with modification
the idea that species change over time, give rise to new species, and share a common ancestor
What does descent with modification lead to
production of new genes and new traits and splitting of lineages into new species
is evolution change within individuals?
no
What is phenotypic plasticity
- changes in an organisms behaviour, morphology, and physiology in response to a unique environment
- ability of a genotype to express different phenotypes depending on the environment
what are the causes of evolution?
selection
mutation
migration
drift
What is selection
the only known cause of design
What is mutation
“fuel” of evolution
random
What is migration
quick way to get “fuel” (mutations)
what is drift
powerful retarding force, random
- change in allele frequency within a population over time
is evolution synonymous with natural selection
no
what is evolutionary fitness (Darwinian fitness)
an individuals relative contribution of alleles to the next generation
What is evolutionary fitness a function of
p (survival)
E (number of offspring)
What is adaptation
a trait that causes an increase in fitness relative to other real or imagined traits via its relatively good fit to a particular environment
what are Darwins 4 postulates for evolution by natural selection
- individuals vary in phenotype
- some phenotypic variation is passed on to offspring
- more offspring are produced that can survive or reproduce
- survival and reproduction is not random, but is related tp aspects of phenotypic variation
Are humans particularly variable
not particularly for size
what is heritability
degree to which individuals are similar because they have the same genotype
What is a good way to measure heritability
cross-fostering or twin experiments
what must occur if there is a differential transmission of genetic material mediated by the environment
evolution by natural selection
What is differential fitness
that survival and reproduction vary between individuals
Why is HIV fatal to humans
- evolution by natural selection has no foresight
- transmission allows HIV to persist even though host dies
- there hasn’t been enough time for humans to evolve resistance
- there hasn’t been enough time for co-evolution to occur between humans and HIV
When will there be no natural selection on a trait
if there is no variation, if variation isn’t heritable, and if variation is heritable but it doesn’t differentially affect survival or reproduction
do individuals evolve
no
does selection act for the good of the lineage
no
does natural selection look ahead
no
does natural selection create variation
no, it actually erodes variation by selecting against trait s
what creates variation
mutations
what causes gene frequencies to change
mutation
what are the types of variation
genetic, environmental
what is genetic variation
variation due to different alleles at a locus
fuel needed
fuel needed to power evolution by natural selection powered by mutations
what is environmental variation
variation due to environments
is environmental variation
heritable
What is genotype by environment variation
variation due to interactions between genes and the environment
can also be fuel for selection since phenotypic plasticity can be adaptive
what is a mutation
any change in the nucleotide sequence
how do you know if a mutation is heritable
check if its a germ line mutation
what is a germ line mutation
mutation occurs in an egg or sperm cell
what happens if a mutant cell is incorporated in a zygote
all cells of the progeny will contain the mutation
what is a somatic mutation
mutation that occurs in a body cell other than egg/sperm
occurs in one cell and then is passed on via cell division
what are the types of mutations
point mutation insertion deletion duplication inversion chromosome fusion aneuploidy/ polyploidy
What is a point mutation
a single base pair change from one nucleotide to another
what causes point mutations
external factors that damage DNA followed by polymerase repairing it “incorrectly”
errors during DNA replication by polymerase enzymes
and then these mutations must evade corrections to become persistent mutations
what type of mutation is Huntington’s disease an example of
insertion
what type of mutation is cystic fibrosis an example of
deletion
what is a gene duplication
a segment of dna is copied more than once
what causes gene duplications
usually caused by an unequal crossing over or retroposition
what is retroposition
a mechanism that creates duplicate gene copies in new genomic positions through reverse transcription of mRNAs from source genes
what leads to copy number variation
duplication
what is copy number variation
phenomenon in which sections of the genome are repeated and the number of repeats vary among individuals
what are copy number variations associated with
disease in humans and rapid evolution
what is an inversion
a region of DNA that has been flipped so genes are in reverse order
What cause inversions
faulty repair
what happens when one chromosome copy contains inversions and the other doesn’t
they cannot align properly during meiosis, resulting in very little crossing over. When crossing over does occur offspring typically cannot reproduce since they are missing genes
why do inversions tend to be inherited as a unit
since inversions lead to lower levels of crossing over, causing tighter linkage among loci within the inversion
what is human chromosome 2 a result of
end-to-end fusion of two ancestral chromosomes
what is aneuploidy
when chromosomes are lost leading to an abnormal number of chromosomes
what is polyploidy
when chromosomes are duplicated leading to an abnormal number of chromosomes
what is a - s mean
means it is selected against
what is a + s
means it is selected for
when do most mutations occur
during cell division
where do 2/3 of new mutations in humans come from
males since sperm is associated with more cell divisions than eggs
what organs are most likely to get cancer
organs with more cell divisions carry more somatic mutations
what is the average germ line mutation rate
1.0x10^-8
how many basepairs is a haploid human genome
3.2x10^9 base pairs
is genetic drift the result of selection
no
is genetic drift adaptive
no
what is genetic drift
random process that results in a change of allele frequency
a random sampling error that in the production of zygotes from a gene pool
what is a sampling error
random discrepancy between theoretical and actual results
what are the causes of drift
continuous (background) drift
Founder effect
population bottleneck
what is continuous drift
just like from one generation to the next, some people have offspring and some dont, some alleles get passed
what is a founder effect
when a small group of individuals become geographically isolated from the remainder of the population
or a small group of individuals colonize a new site
what is a population bottleneck
a major reduction in population size which normally reduces genetic variation because at least some alleles are lost (especially rare ones)
are age effects of drift greater in bigger or smaller populations
smaller
What is fixation
when one allele goes tp 100% frequency
change in gene pool from a state with multiple alleles to a state with only one
does fixation occur faster is smaller or bigger populations
smaller
what is heterozygosity
the possession of two different alleles of a particular genes
What happens to heterozygosity as alleles drift
it increases
what is effective population size affected by
number of adults
sex ratio of breeders
fluctuations over time
what are things that depress effective population size (Ne)
make the population genetically smaller than how it looks
variation in population size, variation in sex ratio, variations in family size
what is inbreeding
mating with relatives
what causes inbreeding
breeding systems
small populations
mating systems
what ate the types of non-random mating
assortative mating
disassortative mating
what is assortative mating
individuals choose mates that are phenotypically more similar than is expected by chance
what is disassortative mating
individuals choose mates that are phenotypically less similar than is expected by chance
what are the effects of inbreeding
- increased homozygosity (which exposes recessive alleles to selection)
- greater proportion of offspring will have lower fitness than offspring from outcrossing
what is inbreeding depression
depressed fitness due to deleterious recessive alleles
What can inbreeding accelerate
fixation
why does drift counteract selection
because it is random
why does inbreeding have different effects on different scales
- potentially lowers fitness of the lineage that inbreeds and so is selected against
- causes purging of bad alleles so it can increase fitness at a population level
what is migration
movement of alleles between populations
what causes migration
movement of individuals or gametes followed by mating or fertilization
what is the effect of migration
immediate change in allele frequency in the recipient population
equilibrium is reached rapidly
island population ends up with the migrant allele frequency
usually one migrant/generation is enough to homogenize populations
-in absence of selection (or if alleles are selectively neutral) migration homogenize allele frequencies among populations
what does p stand for
frequency of most common allele (usually the dominant one)
what does q stand for
frequency of less common/ all other alleles
what happens if selection and migration tend to increase frequencies of the same alleles
selection can amplify the effects of migration
what happens if selection and migration are opposed
if selection > migration : then the differences between populations will be maintained even in the face of migration
if migration > selection: differences among populations will be reduced
why is migration important for small populations
since migrant alleles may decrease fitness in the “island” population and thereby slow adaptive evolution. this could be a possible reason for the range limits of species
how can migration speed up evolution
can bring in new alleles
what does s stand for
selection coefficient
