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evolution (typical)
the scientific explanation for biodiversity
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Darwin evolution
new things come from old and are different when they come from them (descent of modification)
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evolution
change in intrinsic properties of a population (built in properties)
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pre-evolutionary ideas
all organisms were individually created and they didn't change individually overtime
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evolutionary ideas
organisms do change over time
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2 important people involved in evolutionary ideas
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2 evolutionary ideas of lamarck
- mutations arise b/c of need
- individuals w/ beneficial mutations produce more offspring
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mutations arise b/c of mutations explained
- if the organism needs a character they get it
- mutations that are useful in the environment will arise in the organism (sometimes)
- random arise of mutations in some individuals
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2 evolutionary ideas of Darwin
- mutations arise randomly w/ respect to their usefulness
- individuals w/ beneficial mutations produce more offspring
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natural selection (2)
- individuals with beneficial mutations produce more offspring
- mutations arise randomly with respect to their usefulness
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mutations, whether they are good or bad, get sorted out overtime
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3 requirements for evolution
- variation must exist
- variation must be heritable
- mechanism for differential spread must exist
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3 mechanisms of differential spread
- random change causes evolution
- movement of variation from one population to another
- mating systems of a population
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adaptation
a good fit between an organism (phenotype) and their environment
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difference between adaptation and evolution
adaptation only arises by NS while evolution can arise in a variety of ways
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ultimate source of variation is mutations and recombination can add mutation on homologous X to a single X
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2 types of recombination
- chromosomal
- sexual reproduction
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HW came up with a test to see if mendel was correct, he wasn't. However, these only apply if no evolution is occuring
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population of inference
to study a group of things you want to know
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sample
a subset of population of inference
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a sample is hard to draw inference from, it needs to be random in order to get good inference
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random sampling
every individual of a population inference has an = chance of being in a sample
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bias sample
only a few certain of a pop inference has an equal chance of being in a sample
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sample error
difference between a measurement taken on a random sample and the same measurement taken on population of inference
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the sampling error is inversely proportional,
- the bigger the sample the less of an error
- the smaller the sample the bigger the error
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sampling error only applies from random sample
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effect of finite population size and allele frequencies
genetic drift
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in finite pop size each new gene is a random sample of the previous gene pool which might look different from the previous generation
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large and diff changes in finite pop size overtime will cause changes which may lead to being fixed or changes in the allele frequency
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pop outcome is less variation overtime if genetic drift is occuring
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5 characters of Genetic drift (random process)
- causes evolution
- reduces and eliminates (w/in a pop) variation
- drift is greater in small pop, will lose variation overtime
- increases between pop genetic variation
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between pop variation meaning
the gene pool has similar ps and qs, shares the same alleles at the same frequency
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between pop variation start = 0
there is no difference in the beginning
however it goes up over time (variation)
it continues until no genetic variability left
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allele freq for species as a whole
if isolated individuals overtime preserves variation they save more variation than they do when in a population as a whole
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locus
spot on the X where the gene is
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allele
one or more forms of a gene
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founder effect
change in allele freq caused by founding a new pop with a small # of individuals
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4 examples of the founder effect
- ellis van crevald
- hemophilia
- cohen syndrome
- 5-alpha-reductive deficiency
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ellis van crevald
genetic disease (homo) such as deformities, heart complications, dwarfism, etc.
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small pop increases in genetic diseases, but why is it not vice versa
ascertainment bias
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ascertainment bias
easier to see an increase than to see a decrease in these rare alleles, so we only study those that are in a society
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3 reasons why selection doesn't eliminate non-favorable diseases that are genetic and recessive
alleles can hide in a heterozygote
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random mate
probability of mating with an individual vs mating w/ a different individual
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inbreeding
when relative mate, or some aspect of relative mating
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assertive mating
individuals w/ similar phenol are more likely to mate that you would expect by chance alone
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disassortive mating
individuals w/different phenol mate more than expected by chance alone
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inbreeding increases homozygotes which causes more recessive alleles to come out
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identical by dissent
identical due to being descend from a single gene in the past
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identity in state
identical in state but different bc they come from different genes of the past
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autozygote
3 individual with both copies of a gene, identical by dissent
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in order to see if genes go to another gene you
will need to get a pedigree
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inbreeding coefficient f
probability of hetero of one individual
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inbreeding coefficient F
- probability of the pop being hetero
- *can only be calculated from pedigrees*
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inbreeding depression
decrease in fitness in an inbreeding pop
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2 causes of inbred depression
- increase homo for recessive deleterious alleles at a few loci, not all loci same
- decrease hetero at most or all loci
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as the environment changes, what will happen when it comes to the organism and their being in the environment
mutations will arise that are beneficial in the environment
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mutations that are useful in the environment will arise in the organisms only in some if needed
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beneficial mutations will arise while non-beneficial mutations will disappear
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evolution requirements is used to
bring rare forms of a trait to become common and common to become rare
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recombination function
takes different copies of a X and mixes them up to create variation
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variation arise due to the environment because of need
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the results of the replica plating experiment
shows that antibiotic resistance pre-existed before its exposure to antibiotic
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genotype
a set of alleles that individuals have at every one or more loci
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it only takes 1 gen to get the hardy Weinberg theorem in alleles, but 2 in genotypes
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HW is only applicable if no other force is acting upon it
Genetic drift is the same as well
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sampling error is also the chance it will be random from population if inference
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genetic drift cause by finite pop is
change in allele frequency
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finite pop causes evolution
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all real pop evolve by genetic drift
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GD eliminates variation in a pop
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less variation in an organism means the organism will be less likely to adapt to their environment
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isolated populations overtime preserve variation more than populations that are all grouped together
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homozygosity will go up is there is inbreeding
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do inbreds have more problems than individuals who do not interbreed
they are around an even amount, highly inbred individuals are the same fitness as those that are not inbred
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if you are auto then you are less fit, you may suffer from inbreeding depression
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why do we still have deleterious alleles in a pop
because those alleles hide in heterozygotes, if a pop starts to inbreed then the more homozygotes for the allele increases causing the deleterious alleles to appear in a population
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if negative slope
inbreeding depression
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if positive slope
no inbreeding depression
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Ideal individuals
assumptions made
- finite constant pop size
- poisson distribution production of offspring
- hardy weinberg
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problems with ideal individuals (2)
- there are no ideal individuals
- pop size is not always constant
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poisson distribution production of offspring depends on whether or not they produce offspring
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effective pop size
is the equivalent # of ideal individuals that will accumulate inbreeding at the rate real pop accumulate inbreeding
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pop bottle neck
sharp reduction in size of a pop due to environmental random events
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founder effect
the reduced genetic diversity that results when a population is descended from a small number of colonizing ancestors.
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inbreeding of pop is inversely proportional to effective pop size
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is it possible effective pop size to be smaller than the actual pop size
F
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a pop that doesn't inbreed will have an increase in effective pop size than the actual pop size
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inbreeding does not cause the loss of alleles, finite pop (drift) size loses alleles
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gene flow
movement of genes from one pop to another
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gene flow with genetic drift take a long time before variation is lost and alleles become fixed
sometimes pop gene flow move together to go through variation similarly to each other
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how is gene flow opposite from genetic drift
because gene flow causes allele frequency changes and it increases in genetic variation why GD gets rid of variation
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(2) direct methods of measuring gene flow
- experimental studies
- observational studies
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experimental studies
studies in which the environment gets manipulated
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Pros of direct methods of measuring gene flow (2)
- inexpensive and easy
- estimate current gene flow
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Cons of direct methods of measuring gene flow (4)
- manipulation may effect results
- movement is not necessarily gene flow
- hard to measure rare gene flow
- estimate current gene flow
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Gene flow increase
Gene flow decrease
- pop should be similar genetically
- pop should not be similar genetically
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Fst
means diff in allele freq among pop
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variance
the difference in pop average squared deviation from the mean
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p (with line over)
average p fir the whole set of pop maximum possible value the different could be
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this kind of mating increase homozygosity and decrease hetero
decrease homo and increases hetero
- assertive mating
- dis-assertive mating
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hetero is more fit than homo because
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you can never get a steady state when it comes to inbreeding because you cant select against them
you cant favor good genes after getting rid of bad genes
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inbreeding + selection do what to alleles
decrease allele freq selection
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you can drive an allele into low freq but they will never be fully eliminated due to hetero
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due to all pop being finite and all other forces occurring at the same time...
all pop have GD going on
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non-random mating occurs by these 3
- inbreeding
- assertive mating
- dis assertive mating
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inbreeding occurs most in what kind of pop
finite pop
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inbreeding cause evolution only in the sense that
of it changing genotype
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why is the first cause of inbreeding being bad the most important
bc how we detect how a pop has inbreeding depression
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how does a stead state occur in a graph comparing inbreeding and noninbreeding pop
the graph may be at a negative slope until the alleles overtime even themselves out to create a steady state
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inbreeding changes geno freq but not allele freq
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Selection eliminates recessive deleterious alleles after a while which causes the flattening out
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Homozygote when it comes to autozygote = not identical by dissent but is identical
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When youre at HW you stay there so your Allele freq don’t change ever, but geno may change around 1 gen
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some selfing plants purge their deleterious alleles which causes them to be at a steady state when graphed compared to non inbreeding organisms
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hetero is always better at every locus which means
all alleles are rr deleterious alleles, are more fit than you know
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just because you can select against the homo alleles suggests that you can get rid of them
lost alleles is due to selection getting rid of them
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inbreeding plus selection causes a change in allele freq, inbreeding cant act alone
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with assertive mating no change in allele freq for the loci
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increase in homo in assertive mating when it comes to geno freq
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when inbreeding goes on, you expect homo in every loci
while in assertive you expect an increase in homo for loci effecting the mate choice trait
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in dis assertive mating it causes a decrease in homo for
loci affecting the mate choice trait
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1 difference in allele freq of assertive and dis
- assertive have no allele freq change
- dis changes allele freq
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assortive redistributes alleles but does not affect freq
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in disassortive mating individuals that look for common mates is harder then trying to find a different mate which causes allele freq to
move toward the middle (50/50 or an even amount when divided between them)
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random mating in a small pop can cause
- inbreeding
- ex gazelles, 4 pop, mate with who ever to increase heard
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how to cal the amount of inbreeding you will get
F = 1-(1-1/2N)^t
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small pop have inbreeding occur which will lead to inbreeding depression at a faster rate
small pop will also have GD causing a lack of variation to occur within the pop
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mutations that decrease inbreeding may cause
an increase in effective pop size
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each individual has the same probability of chance reproducing but they don't always reproduce
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decrease rate of inbreeding by equalizing the # of individuals reproducing
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behaviors that increase inbreeding will decrease the effective pop size and vice versa
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if you equalize the amount of reproduction among individuals you will double the effective pop size
the cut the rate in half of the accumulation of inbreeding
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finite pop causes accumulation of inbreeding and loss of alleles, not inbreeding alone.
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if p1=p2
if p1>p2
if p2>p1
- there will be no change in each other
- they will go up as one goes down so they can make themselves more similar to each other
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_______has the property of making pops become more similar
gene flow
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finite pop size causes these 2
- causes alleles to become lost in a pop
- causes individuals to be more auto (inbreeding)
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drift causes the loss of alleles not inbreeding
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