envs lecture 7 Flashcards
what is genetic drift
evolution at random
what is coalescence (w/r to time)
backward in time
what is genetic drift w/r to time
forward in time
poster child of genetic drift
elephant seals
what are one of the least genetically variable mammals (recent)
northern elephant seals
whats up w/ elephant seals
overhunting reduced their population to 40 –> extreme bottleneck
whats up w/ genetic variability in elephant seals
lack of genetic variability
what two issues have caused lack of genetic variability
overhunting & bottleneck AND small effective population size
why do seals have small effective population size
because only few males succesfully mate
what is genetic drift
describes effects of sampling errors on allele frequencies due to chance survival, reproduction, inheritance events
when is genetic drift important
when some H-W assumptions are false
what H-W assumptions are false
generations overlap, non-random mating, uneven sex ratios, small population size
what does uneven sex ratios mean
diff numbers of females and males
what do we need in order to estimate drift
number of breeding individuals AKA individuals that contribute alleles to succeeding generations AKA Ne
basically what is genetic drift
evolutionary process, describes effects of sampling errors on allele frequencies due to chance events
what are chance events
related to survival, reproduction, inheritance of alleles
what are these chance events like
coin tosses
when are the effects of genetic drift important
when some HWE assumptions are false
describe genetic drift
bag of marbles, first draw is 6:4. next draw is 7:3, then last draw is 4:6
what does genetic drift do
random sampling over several generations, this changes allele frequencies in populations
describe the simulations
two alleles that start out at equal 50:50 frequencies.
what is the first thing to notice at the start of next gen
allele frequencies change by random sample of genes (drift causes allele frequencies to randomly change)
describe drift (is it biased or unbiased), and how does this affect allele frequencies
drift is random and unbiased, allele frequencies equally likely to go up or down
what is genetic drift
random fluctuations in allele frequencies
what is drift in small populations
drift is larger /stronger (random fluctuations in allele frequency)
what does drift cause
causes populations that were identical to become different
what happens with genetic drift
variation is lost
how do we know variation is lost
because it moves away from 50:50 allele frequencies
basically what does drift cause
causes populations to differentiate by fixation of alleles w/o action of natural selection
what does drift do
allele fixation
does drift cause allele fixation with or without selection
without natural selection
describe drift when populations are hella large
drift is weak
what happens in the first generation in a sample
nice even distribution of allele frequencies, 50:50
what happens as time goes on
distributions are spread, fixed for one allele or another
what does the time it takes to reach allele fixation vary with
increases with population size (more population, longer it takes to reach allele fixation)
what happens if this process/sample runs across many genetic loci
genetic drift causes populations to diverge
what happens to a sample simply by drift
these populations accumulate differences in frequency of allele, and fixation occurs
basically what is genetic drift
evolution at random
how can you trace evolutionary history of every gene in your genome
by determining which gene copy at a given locus you inherited from your mom, which one from dad, and go back in time for every gene
what happens if you do this for everyone
for any locus in the genome, there was a copy of that gene at some time in the past that was ancestor of all copies of that gene now carried by all living humans
what is coalescence
tracing the genealogy/ancestry of gene copies thru time, all ‘living’ copies of a given gene in a population are ultimately descendants of a single ancestor
whats up w/ all living copies of a given gene
ultimately descendants of a single ancestor
when do things coalesce
when lineages of two gene copies merge
what does each diploid individual carry
carries two copies of every given gene, one from mom one from dad
5 diploid individuals means how many genes
10
describe whats going on in this example
no selection; difference in # of descendants left by diff copies of gene are random –> genetic drift
describe the pic
first generation there were 9 other gene copies (10 total), but only 1 was the ancestor, other 9 left no descendants
mtDNA
inherited maternally, we get mtDNA from mothers not fathers
what is mitochondrial eve
if you trace all human mtDNA back in time to most recent common ancestor
where there other females who lived during mitochondrial eve
yeah, but didn’t contribute their mtDNA to currently living humans
did those females contribute other genes to modern humans?
yesssss
when did mitochondrial eve live
125,000 years ago
can we do this for ancestry of Y chromosome
ya, can find single male human ancestor
what does this show
ancestor of all mtDNA in living humans was female, ancestor of all Y chromosomes was carried by a male
what does this ^^ prove
diff genes can have diff genealogies and common ancestors
what do any two copies of gene share
share an ancestor
what do diff genes have
diff genealogies
does gene trees match species trees
not always
what is the average time to common ancestor
2Ne generations [if no selection]
what is Ne
effective population size
what does it mean for gene to evolve neutrally
no selection
what does it mean the larger the population size
longer time it takes for two copies to coalesce at a common ancestor
why is there a lot of variation in avg coalescence time for diff pairs of genes
b/c drift is random, coalescence evolves drift
did mitochondrial eve and Y chromosomal Adam live in same population
nope; diff times
when was Y chromosomal Adam
190,000 years ago
does coalescence still apply if selection is acting
yup
what changes if selection is acting
it changes the time to common ancestor
do gene trees always match species trees
not always
give 2 examples
one example, gene tree matches species tree (species B and C are most recent common ancestor and genes coalesce); other example B and C most close relatives, but A and B genes coalesce)
what results in diff gene tree & species tree
deep coalescence in combo w/ incomplete fixation of gene lineages within species lineages (incomplete lineage sorting)
why does genealogy of genes not match species tree
random process of lineage sorting that incorrectly sorts alleles (like mutation)
lineage sorting
lineage sorting of ancestral polymorphism can cause mismatch of species tree and gene tree
what is lineage sorting caused by
genetic drift
what is strength of genetic drift driven in part by
effective population size
what is strength of genetic drift measured by
Ne
what is Ne
of individuals that would give idealized population the same strength of drift as an actual population of interest
is Ne same size or bigger/smaller than actual pop
always smaller
why is Ne always less than actual
populations fluctuate in size, uneven sex ratio, young&old don’t reproduce, variable reproductive success (some more successful than others)
what is one reason Ne is less than actual
populations fluctuate in size
what is another reason Ne is less than actual
uneven sex ratio (not 1:1)
what is yet another reason Ne is less than actual
too young & old don’t reproduce
aaand another reason Ne is less than actual
variable reproductive success in breeding age males & females (some are more successful than others, more offspring than others)
whats another reason
limited dispersal from birthplace (dispersal of individuals away from their birth place is limited)
what does small Ne mean
strong drift
what does large Ne mean
weak drift
whats up w/ infinitely large population
immune to drift
whats up w/ population size being one of the reasons Ne is smaller than actual population
populations fluctuate, leading to Ne being smaller than actual
whats up w/ population size
pop size may be occasionally low, accentuating genetic drift (like northern elephant seal)
what 2 things impact populations fluctuating (and thus Ne being smaller)
bottleneck and founder effect
what do both bottleneck and founder effect do
both reduce genetic variation
what is bottleneck
pop is reduced to small size for a few generations
what is founder effect
genetic drift that accompanies start of new pop where a founder colonizes a new area. allele may not be included in new population, or under/or over represented by chance
what are 2 things that cause massive fluctuations in population size
bottlenecks and founder effects
whats up w/ alleles in founder effects
founding population that colonizes new island may be missing an allele, so its under represented
what is small founding population subject to
rapid fixation/loss of alleles
what do loci tend towards in small populations
homoallelism (monomorphism)
what do small populations tend toward
decreased variability, less for selection to act on
what is there a lower chance of in small populations
lower chance of mutation generating new alleles because there are fewer individuals
real life example of a founder event
zebra finch (in australia)
what is pi
nucleotide diversity, measure of heterzygosity/genetic diversity
what can pi tell us about
genetic diversities of lineagse
what is heterozygosity (pi) a chance of
chance that two chromosomes in a population have different nucleotides at a given site (measure of genetic diversity)
what does human genetic variation decrease with
distance from Africa
why does human genetic variation decrease w/ distance
b/c multiple founder events reduced population size
what can measures of heterozygosity tell us about
population expansion and founder events (like humans expanding out of Africa and colonizing rest of world)
what is human genetic variation measured in
heterozygosity
where is diversity highest
at the source
where is diversity lowest
furthest away from source
what happens as colonization occurs
creates multiple founder events, reduces population sizes, reduces genetic variation in these small founding populations
what’s another reason Ne is smaller than actual
variable reproductive success
what do successfully breeding individuals show
variation in reproductive success
why do successfully breeding individuals show variation in reproductive success
sometimes at random, sometimes cuz of selection
what happens as a result of variation in reproductive success
some parents donate more alleles to next gen than others, reducing Ne
what is another key factor in causing Ne to be smaller than actual
uneven sex ratio
why do sex ratios vary
not always 1:1; sometimes sex ratio at birth is biased.
another reason why sex ratios vary
females and males survive differently
give an example of low effective population size
in fisheries
what is the fate of advantageous mutations in a population determined by
nat selection, genetic drift
what does genetic drift add
random component to trajectory of frequency of a given mutation
when is drift stronger
smaller effective population szie
what is y axis
allele frequency
what is x axis
number of generations
describe the number of generations to fixation by selection when N is large
constant
describe number of gens to fixation when N is smaler
of generations to fixation is related to N
when does it take more generations for fixation to occur, bigger N (50?) or smaller N (5?)
bigger
more population means
takes more generations for fixation to occur
what does time for fixation of one of two alleles at a locus depend on
p (frequency of ne allele) and Ne
what is fixation time proportional to
effective population size (Ne)
when is time to fixation of one allele maximized
when p (frequency of one allele) is 0.5
large organisms tend to have what (w/r to Ne)
smaller Ne
who has biggest Ne
E.coli (bacteria)
what’s nematodes Ne
doesn’t self fertilize, has bigger Ne than C. elegans
what does self-fertilizing do to Ne
reduces N
describe how polymorphism is distributed across the genome
unevenly
what is much of the polymorphism we see when comparing DNA sequences within species from
random genetic drift acting on selectively neutral mutations
what is mean heterozygosity a measure of
measure of genetic variation
how is polymorphism spread across genome
unevenly
describe how much of base pairs are identical between two randomly chosen huans
99.9% identical
what is mean heterozygosity in human populations
0.45-0.75
what are differences between two humans as high as
1.6%
what are SNPs
single nucleotide polymorphisms
how are SNPs distributed
non-randomly distributed across locus
do exons have less or more variation
less variation
do introns have less or more variation
more
what are exons
coding regions
what are introns
non-coding regions
why do we see this non-random distribution of polymorphisms
mutations in coding regions cause AA changes
what mutations are selectively neutral
mutations in non-coding regions (introns) or in parts of exons that don’t change AAs (like 3rd position)
what happens to these selectively neutral mutations
polymorphism evolves via genetic drift
what are mutations that are NOT selectively neutral
mutations in coding regions that can cause AA changes (so they change proteins too)
what happens to these non-selectively neutral mutations
there are constraints that select against these mutations (cuz they are bad)
what happens to selectively neutral mutations
evolve via genetic drift
what is expected heterozygosity
heterozygosity resulting from neutral mutations evolved by drift in a diploid organism
equation for expected heterozygosity
pi = 4Ne Un
pi
heterozygosity
Un
neutral mutation rate
what is neutral mutation rate
chance per generation that the locus mutates to another allele that does not change an organisms fitness –> so its neutral
what is Ne
effective pop size (which measures drift)
what increases with Ne and Un
polymorphism
what happens to deleterious mutations
weeded out by purifying selection
what happens to loci that experience purifying selection
under selective constraint
describe heterozygosity in non-coding regions
heterozygosity is typically higher
why is heterozygosity higher in non-coding regions
b/c neutral mutation rate approaches actual mutation rate cuz there is barely any purifying selection
what reduces polymorphism across populations
both background selection and selective sweeps
what are selective sweeps
strong positive selection on a beneficial allele causes that allele to go to fixation
what happens as a result of selective sweeps
genetic variants/mutations located near beneficial allele also increase
where is heterozygosity reduced by selective sweeps & background selection
near center and the ends
why is heterozygosity reduced near center and ends
because recombination is lower
where is selective sweeps and background selection stronger
where there is less recombination
why are selective sweeps and background selection stronger where recombination is lower
cuz selectively advantageous/disadvantageous alleles are in stronger linkage disequilibrium w/ nearby alleles when there’s less recombination
describe heterozygosity of ants and vertebrates
lower heterozygosity (0.2-1&)
describe heterozygosity of butterflies and bivalves
higher heterozygosity (1-10%)
what is heterozygosity related to
lower population size, lower fecundity (means lower heterozygosity)
what happens with higher effective population size
drift is weaker
what happens when Ne is higher, drift is weaker
fixation due to selection proceeds more slowly
what happens when Ne is lower and drift is stronger
selection acts more quickly to drive alleles to fixation
describe selection & drift for species w/ large Ne
selection is much more powerful than drift
what does selection being more powerful than drift lead to
precise adaptations like codon bias
codon bias
among synonymous codons ,one is more efficient during translation, and so we see bias towards efficient codons
basically what is codon bias
selection for efficient codons
describe what happens in closely related species
half of AA differences in proteins evolved by positive selection, other half fixed by drift
what is more important in closely related species
selection
what happens for species with small N
most fixation is by drift
how much of differences result from nat selection (for small N)
only 15%
what can drift cause (negatively)
deleterious mutations to spread to fixation
what effect does drift causing fixation of deleterious mutations have
problems for wild populations that go thru bottlenecks
what dose introducing ppl from other populations do to inbred population
reintroduces alleles that had been lost to drift
what does reintroducing these alleles lead to
increased survival of offspring
