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evolution > envs lecture 7 > Flashcards

envs lecture 7 Flashcards

1
Q

what is genetic drift

A

evolution at random

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2
Q

what is coalescence (w/r to time)

A

backward in time

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3
Q

what is genetic drift w/r to time

A

forward in time

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4
Q

poster child of genetic drift

A

elephant seals

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5
Q

what are one of the least genetically variable mammals (recent)

A

northern elephant seals

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6
Q

whats up w/ elephant seals

A

overhunting reduced their population to 40 –> extreme bottleneck

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7
Q

whats up w/ genetic variability in elephant seals

A

lack of genetic variability

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8
Q

what two issues have caused lack of genetic variability

A

overhunting & bottleneck AND small effective population size

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9
Q

why do seals have small effective population size

A

because only few males succesfully mate

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10
Q

what is genetic drift

A

describes effects of sampling errors on allele frequencies due to chance survival, reproduction, inheritance events

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11
Q

when is genetic drift important

A

when some H-W assumptions are false

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12
Q

what H-W assumptions are false

A

generations overlap, non-random mating, uneven sex ratios, small population size

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13
Q

what does uneven sex ratios mean

A

diff numbers of females and males

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14
Q

what do we need in order to estimate drift

A

number of breeding individuals AKA individuals that contribute alleles to succeeding generations AKA Ne

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15
Q

basically what is genetic drift

A

evolutionary process, describes effects of sampling errors on allele frequencies due to chance events

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16
Q

what are chance events

A

related to survival, reproduction, inheritance of alleles

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17
Q

what are these chance events like

A

coin tosses

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18
Q

when are the effects of genetic drift important

A

when some HWE assumptions are false

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19
Q

describe genetic drift

A

bag of marbles, first draw is 6:4. next draw is 7:3, then last draw is 4:6

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20
Q

what does genetic drift do

A

random sampling over several generations, this changes allele frequencies in populations

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21
Q

describe the simulations

A

two alleles that start out at equal 50:50 frequencies.

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22
Q

what is the first thing to notice at the start of next gen

A

allele frequencies change by random sample of genes (drift causes allele frequencies to randomly change)

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23
Q

describe drift (is it biased or unbiased), and how does this affect allele frequencies

A

drift is random and unbiased, allele frequencies equally likely to go up or down

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24
Q

what is genetic drift

A

random fluctuations in allele frequencies

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25
Q

what is drift in small populations

A

drift is larger /stronger (random fluctuations in allele frequency)

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26
Q

what does drift cause

A

causes populations that were identical to become different

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27
Q

what happens with genetic drift

A

variation is lost

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28
Q

how do we know variation is lost

A

because it moves away from 50:50 allele frequencies

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29
Q

basically what does drift cause

A

causes populations to differentiate by fixation of alleles w/o action of natural selection

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30
Q

what does drift do

A

allele fixation

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31
Q

does drift cause allele fixation with or without selection

A

without natural selection

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32
Q

describe drift when populations are hella large

A

drift is weak

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33
Q

what happens in the first generation in a sample

A

nice even distribution of allele frequencies, 50:50

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34
Q

what happens as time goes on

A

distributions are spread, fixed for one allele or another

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35
Q

what does the time it takes to reach allele fixation vary with

A

increases with population size (more population, longer it takes to reach allele fixation)

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36
Q

what happens if this process/sample runs across many genetic loci

A

genetic drift causes populations to diverge

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37
Q

what happens to a sample simply by drift

A

these populations accumulate differences in frequency of allele, and fixation occurs

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38
Q

basically what is genetic drift

A

evolution at random

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39
Q

how can you trace evolutionary history of every gene in your genome

A

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

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40
Q

what happens if you do this for everyone

A

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

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41
Q

what is coalescence

A

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

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42
Q

whats up w/ all living copies of a given gene

A

ultimately descendants of a single ancestor

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43
Q

when do things coalesce

A

when lineages of two gene copies merge

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44
Q

what does each diploid individual carry

A

carries two copies of every given gene, one from mom one from dad

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45
Q

5 diploid individuals means how many genes

A

10

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46
Q

describe whats going on in this example

A

no selection; difference in # of descendants left by diff copies of gene are random –> genetic drift

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47
Q

describe the pic

A

first generation there were 9 other gene copies (10 total), but only 1 was the ancestor, other 9 left no descendants

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48
Q

mtDNA

A

inherited maternally, we get mtDNA from mothers not fathers

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49
Q

what is mitochondrial eve

A

if you trace all human mtDNA back in time to most recent common ancestor

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50
Q

where there other females who lived during mitochondrial eve

A

yeah, but didn’t contribute their mtDNA to currently living humans

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51
Q

did those females contribute other genes to modern humans?

A

yesssss

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52
Q

when did mitochondrial eve live

A

125,000 years ago

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53
Q

can we do this for ancestry of Y chromosome

A

ya, can find single male human ancestor

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54
Q

what does this show

A

ancestor of all mtDNA in living humans was female, ancestor of all Y chromosomes was carried by a male

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55
Q

what does this ^^ prove

A

diff genes can have diff genealogies and common ancestors

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56
Q

what do any two copies of gene share

A

share an ancestor

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57
Q

what do diff genes have

A

diff genealogies

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58
Q

does gene trees match species trees

A

not always

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59
Q

what is the average time to common ancestor

A

2Ne generations [if no selection]

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60
Q

what is Ne

A

effective population size

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61
Q

what does it mean for gene to evolve neutrally

A

no selection

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62
Q

what does it mean the larger the population size

A

longer time it takes for two copies to coalesce at a common ancestor

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63
Q

why is there a lot of variation in avg coalescence time for diff pairs of genes

A

b/c drift is random, coalescence evolves drift

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64
Q

did mitochondrial eve and Y chromosomal Adam live in same population

A

nope; diff times

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65
Q

when was Y chromosomal Adam

A

190,000 years ago

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66
Q

does coalescence still apply if selection is acting

A

yup

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67
Q

what changes if selection is acting

A

it changes the time to common ancestor

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68
Q

do gene trees always match species trees

A

not always

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69
Q

give 2 examples

A

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)

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70
Q

what results in diff gene tree & species tree

A

deep coalescence in combo w/ incomplete fixation of gene lineages within species lineages (incomplete lineage sorting)

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71
Q

why does genealogy of genes not match species tree

A

random process of lineage sorting that incorrectly sorts alleles (like mutation)

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72
Q

lineage sorting

A

lineage sorting of ancestral polymorphism can cause mismatch of species tree and gene tree

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73
Q

what is lineage sorting caused by

A

genetic drift

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74
Q

what is strength of genetic drift driven in part by

A

effective population size

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75
Q

what is strength of genetic drift measured by

A

Ne

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76
Q

what is Ne

A

of individuals that would give idealized population the same strength of drift as an actual population of interest

77
Q

is Ne same size or bigger/smaller than actual pop

A

always smaller

78
Q

why is Ne always less than actual

A

populations fluctuate in size, uneven sex ratio, young&old don’t reproduce, variable reproductive success (some more successful than others)

79
Q

what is one reason Ne is less than actual

A

populations fluctuate in size

80
Q

what is another reason Ne is less than actual

A

uneven sex ratio (not 1:1)

81
Q

what is yet another reason Ne is less than actual

A

too young & old don’t reproduce

82
Q

aaand another reason Ne is less than actual

A

variable reproductive success in breeding age males & females (some are more successful than others, more offspring than others)

83
Q

whats another reason

A

limited dispersal from birthplace (dispersal of individuals away from their birth place is limited)

84
Q

what does small Ne mean

A

strong drift

85
Q

what does large Ne mean

A

weak drift

86
Q

whats up w/ infinitely large population

A

immune to drift

87
Q

whats up w/ population size being one of the reasons Ne is smaller than actual population

A

populations fluctuate, leading to Ne being smaller than actual

88
Q

whats up w/ population size

A

pop size may be occasionally low, accentuating genetic drift (like northern elephant seal)

89
Q

what 2 things impact populations fluctuating (and thus Ne being smaller)

A

bottleneck and founder effect

90
Q

what do both bottleneck and founder effect do

A

both reduce genetic variation

91
Q

what is bottleneck

A

pop is reduced to small size for a few generations

92
Q

what is founder effect

A

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

93
Q

what are 2 things that cause massive fluctuations in population size

A

bottlenecks and founder effects

94
Q

whats up w/ alleles in founder effects

A

founding population that colonizes new island may be missing an allele, so its under represented

95
Q

what is small founding population subject to

A

rapid fixation/loss of alleles

96
Q

what do loci tend towards in small populations

A

homoallelism (monomorphism)

97
Q

what do small populations tend toward

A

decreased variability, less for selection to act on

98
Q

what is there a lower chance of in small populations

A

lower chance of mutation generating new alleles because there are fewer individuals

99
Q

real life example of a founder event

A

zebra finch (in australia)

100
Q

what is pi

A

nucleotide diversity, measure of heterzygosity/genetic diversity

101
Q

what can pi tell us about

A

genetic diversities of lineagse

102
Q

what is heterozygosity (pi) a chance of

A

chance that two chromosomes in a population have different nucleotides at a given site (measure of genetic diversity)

103
Q

what does human genetic variation decrease with

A

distance from Africa

104
Q

why does human genetic variation decrease w/ distance

A

b/c multiple founder events reduced population size

105
Q

what can measures of heterozygosity tell us about

A

population expansion and founder events (like humans expanding out of Africa and colonizing rest of world)

106
Q

what is human genetic variation measured in

A

heterozygosity

107
Q

where is diversity highest

A

at the source

108
Q

where is diversity lowest

A

furthest away from source

109
Q

what happens as colonization occurs

A

creates multiple founder events, reduces population sizes, reduces genetic variation in these small founding populations

110
Q

what’s another reason Ne is smaller than actual

A

variable reproductive success

111
Q

what do successfully breeding individuals show

A

variation in reproductive success

112
Q

why do successfully breeding individuals show variation in reproductive success

A

sometimes at random, sometimes cuz of selection

113
Q

what happens as a result of variation in reproductive success

A

some parents donate more alleles to next gen than others, reducing Ne

114
Q

what is another key factor in causing Ne to be smaller than actual

A

uneven sex ratio

115
Q

why do sex ratios vary

A

not always 1:1; sometimes sex ratio at birth is biased.

116
Q

another reason why sex ratios vary

A

females and males survive differently

117
Q

give an example of low effective population size

A

in fisheries

118
Q

what is the fate of advantageous mutations in a population determined by

A

nat selection, genetic drift

119
Q

what does genetic drift add

A

random component to trajectory of frequency of a given mutation

120
Q

when is drift stronger

A

smaller effective population szie

121
Q

what is y axis

A

allele frequency

122
Q

what is x axis

A

number of generations

123
Q

describe the number of generations to fixation by selection when N is large

A

constant

124
Q

describe number of gens to fixation when N is smaler

A

of generations to fixation is related to N

125
Q

when does it take more generations for fixation to occur, bigger N (50?) or smaller N (5?)

A

bigger

126
Q

more population means

A

takes more generations for fixation to occur

127
Q

what does time for fixation of one of two alleles at a locus depend on

A

p (frequency of ne allele) and Ne

128
Q

what is fixation time proportional to

A

effective population size (Ne)

129
Q

when is time to fixation of one allele maximized

A

when p (frequency of one allele) is 0.5

130
Q

large organisms tend to have what (w/r to Ne)

A

smaller Ne

131
Q

who has biggest Ne

A

E.coli (bacteria)

132
Q

what’s nematodes Ne

A

doesn’t self fertilize, has bigger Ne than C. elegans

133
Q

what does self-fertilizing do to Ne

A

reduces N

134
Q

describe how polymorphism is distributed across the genome

A

unevenly

135
Q

what is much of the polymorphism we see when comparing DNA sequences within species from

A

random genetic drift acting on selectively neutral mutations

136
Q

what is mean heterozygosity a measure of

A

measure of genetic variation

137
Q

how is polymorphism spread across genome

A

unevenly

138
Q

describe how much of base pairs are identical between two randomly chosen huans

A

99.9% identical

139
Q

what is mean heterozygosity in human populations

A

0.45-0.75

140
Q

what are differences between two humans as high as

A

1.6%

141
Q

what are SNPs

A

single nucleotide polymorphisms

142
Q

how are SNPs distributed

A

non-randomly distributed across locus

143
Q

do exons have less or more variation

A

less variation

144
Q

do introns have less or more variation

A

more

145
Q

what are exons

A

coding regions

146
Q

what are introns

A

non-coding regions

147
Q

why do we see this non-random distribution of polymorphisms

A

mutations in coding regions cause AA changes

148
Q

what mutations are selectively neutral

A

mutations in non-coding regions (introns) or in parts of exons that don’t change AAs (like 3rd position)

149
Q

what happens to these selectively neutral mutations

A

polymorphism evolves via genetic drift

150
Q

what are mutations that are NOT selectively neutral

A

mutations in coding regions that can cause AA changes (so they change proteins too)

151
Q

what happens to these non-selectively neutral mutations

A

there are constraints that select against these mutations (cuz they are bad)

152
Q

what happens to selectively neutral mutations

A

evolve via genetic drift

153
Q

what is expected heterozygosity

A

heterozygosity resulting from neutral mutations evolved by drift in a diploid organism

154
Q

equation for expected heterozygosity

A

pi = 4Ne Un

155
Q

pi

A

heterozygosity

156
Q

Un

A

neutral mutation rate

157
Q

what is neutral mutation rate

A

chance per generation that the locus mutates to another allele that does not change an organisms fitness –> so its neutral

158
Q

what is Ne

A

effective pop size (which measures drift)

159
Q

what increases with Ne and Un

A

polymorphism

160
Q

what happens to deleterious mutations

A

weeded out by purifying selection

161
Q

what happens to loci that experience purifying selection

A

under selective constraint

162
Q

describe heterozygosity in non-coding regions

A

heterozygosity is typically higher

163
Q

why is heterozygosity higher in non-coding regions

A

b/c neutral mutation rate approaches actual mutation rate cuz there is barely any purifying selection

164
Q

what reduces polymorphism across populations

A

both background selection and selective sweeps

165
Q

what are selective sweeps

A

strong positive selection on a beneficial allele causes that allele to go to fixation

166
Q

what happens as a result of selective sweeps

A

genetic variants/mutations located near beneficial allele also increase

167
Q

where is heterozygosity reduced by selective sweeps & background selection

A

near center and the ends

168
Q

why is heterozygosity reduced near center and ends

A

because recombination is lower

169
Q

where is selective sweeps and background selection stronger

A

where there is less recombination

170
Q

why are selective sweeps and background selection stronger where recombination is lower

A

cuz selectively advantageous/disadvantageous alleles are in stronger linkage disequilibrium w/ nearby alleles when there’s less recombination

171
Q

describe heterozygosity of ants and vertebrates

A

lower heterozygosity (0.2-1&)

172
Q

describe heterozygosity of butterflies and bivalves

A

higher heterozygosity (1-10%)

173
Q

what is heterozygosity related to

A

lower population size, lower fecundity (means lower heterozygosity)

174
Q

what happens with higher effective population size

A

drift is weaker

175
Q

what happens when Ne is higher, drift is weaker

A

fixation due to selection proceeds more slowly

176
Q

what happens when Ne is lower and drift is stronger

A

selection acts more quickly to drive alleles to fixation

177
Q

describe selection & drift for species w/ large Ne

A

selection is much more powerful than drift

178
Q

what does selection being more powerful than drift lead to

A

precise adaptations like codon bias

179
Q

codon bias

A

among synonymous codons ,one is more efficient during translation, and so we see bias towards efficient codons

180
Q

basically what is codon bias

A

selection for efficient codons

181
Q

describe what happens in closely related species

A

half of AA differences in proteins evolved by positive selection, other half fixed by drift

182
Q

what is more important in closely related species

A

selection

183
Q

what happens for species with small N

A

most fixation is by drift

184
Q

how much of differences result from nat selection (for small N)

A

only 15%

185
Q

what can drift cause (negatively)

A

deleterious mutations to spread to fixation

186
Q

what effect does drift causing fixation of deleterious mutations have

A

problems for wild populations that go thru bottlenecks

187
Q

what dose introducing ppl from other populations do to inbred population

A

reintroduces alleles that had been lost to drift

188
Q

what does reintroducing these alleles lead to

A

increased survival of offspring

evolution (15 decks)

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