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Micro 450 > Unit 3 YIPPEE!!! > Flashcards

Unit 3 YIPPEE!!! Flashcards

1
Q

define evolution

A

change in properties of groups of organisms across generations
descent with modification
change of alleles in a population
NOT natural selection

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2
Q

why study evolution?

A

central organizing principle of biology
human health
technology

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3
Q

Lamarckian Theory of Evolution

A

traits change through use and disuse during the individual’s life: more frequent use leads to strengthening and enlargement.
inheritance of acquired characteristics
acquired traits are a direct effect of environment on an organism

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4
Q

Natural selection

A

pre-existing variations in a population=differential survival and/or reproduction, leads to changed distribution of variants in next generation
DOES NOT create new variants, only acts on already existing variations.
destroys variation by weeding out variants.

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5
Q

Luria-Delbruck Experiment 1943

A

-parellel cultures innoculated with phage-sensitive bacteria
-Hypothesis 1: induced mutation-resistant mutants arise after exposure to the phage. would result in small fluctuations of number of colonies per plate.
-Hypothesis 2: spontaneous mutation-resistant mutants arise in the flask prior to exposure. would result in large fluctuations of number of colonies per plate
Conclusion: mutations arose spontaneously in the flask prior to exposure to phage.

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6
Q

conditions for evolution by natural selection

A
  1. variation in reproductive success among individuals
  2. variation in traits among individuals
  3. partial heritability of traits across generations
  4. correlation between traits and reproductive success
    when conditions are met, distribution of traits in a population will adaptively change across generations
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7
Q

adaptation

A

increase in frequency of a heritable organismal feature because it increases the average survival and/or reproductive success relative to the rest of the population.
is a heritable, common feature in the population

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8
Q

outdated adaptation/vestigial structure

A

adaptation that arose in past environments and no longer increases reproductive success

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9
Q

exaptation

A

feature that performs a function but that was not produced by natural selection for its current use
example: feathers.

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10
Q

non-adaptative mechanisms by which a heritable trait can increase in frequency in a population

A

genetic drift

genetic draft

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11
Q

genetic drift

A

some heritable features become common in a population because of chance not because they increase survival and reproductive success.

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12
Q

hitchhiking/genetic draft

A

some heritable features become common in a population because they were genetically linked to a selected locus (ex on the same chromosome) not because they increase survival and reproductive success.
especially important in asexual populations such as bacterial populations because recombination counteracts this process

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13
Q

Fun facts about natural selection

A

operates on individuals but changes characteristics of population.
consequences occur in the population by changing the distribution of heritable traits
does not act for the future-each generation is the product of adaptations of the previous generation

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14
Q

directional selection

A

favors individuals that vary in one direction from the mean.
examples: selection for large body size of plains cliff swallows, emergence of antibiotic resistance

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15
Q

stabilizing selection

A

favors average individuals
example: human birth weight
NEED MICROBIAL EXAMPLE

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16
Q

disruptive selection

A

favors individuals that vary in both directions from the mean.
important driving force for speciation
example: black bellied seed crackers-long beaked individuals eat large seeds, short beaked eat small seeds., intermediate beaks handle seeds poorly.
MICROBIAL EXAMPLE?!

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17
Q

frequency-dependent selection

A

fitness of a trait depends on its frequency relative to other traits in a population

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18
Q

negative frequency dependence selection

A

purifying selection-purges many deleterious mutations.
as abundance of a trait in population increases, it is less favored by selection. trait more favored when rare.
example: left-jawed fish attack from right side. less frequent in population so more favored.
cooperators and non-cooperators in a snow-drift game.

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19
Q

positive frequency dependent selection

A

as abundance of a trait in the population increases it is more favored by selection. trait more favored when common.
example: poisonous coral snake uses color to warm predators. all snakes must be colored the same for the coloring to be effective.

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20
Q

balancing selection

A

cases when natural selection maintains two or more forms in a population
in sexual populations, heterozygote advantage selects for maintaining traits.

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21
Q

Antibiotic-producing bacteria in liquid vs in agar

A

in liquid: positive frequency dependent selection. common phenotype wins.
in agar: toxin producers outcompete sensitive bacteria independent of initial frequency

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22
Q

genotype

A

organism’s full hereditary information
heritable variation happens only at the level of the genotype.
is the genotype.

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23
Q

phenotype

A

set of actually observed properties of an organism, such as morphology, development, or bahavior
natural selection acts on phenotype
genotype+random factors+environment=phenotype

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24
Q

mutation

A

change in the sequence of a chromosome

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25
Q

horizontal gene transfer: Darwinain or Lamarckian?

A

Darwinian if consider plasmid insertion another type of mutation. like point or deletion then its random.

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26
Q

CRISPR-cas system evolution

A

Lamarkian because environmental factors direct the mutation to create beneficial mutations.
much more powerful than Darnwinian because its faster and you can acquire the exact gene needed.

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27
Q

evolution proceeds through (2 steps)

A
  1. mutations created by variants

2. selection eliminating variants unsuited to their environment

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28
Q

evolvability

A

capacity of a system for adaptive evolution
genotype to phenotype map is evolvable if genetic changes can lead to novel functions that are helpful for survival and reproduction

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29
Q

mechanisms of evolvability (3)

A

innovation sharing through genetic exchange
modularity
redundancy

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30
Q

innovation sharing through genetic exchange

A

DNA can be transferred between organisms–>organisms can acquire novel traits in a single step.
HGT is enabled by the universality of the genetic code.
HGT driven by plasmids, viruses, machinery for DNA uptake

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31
Q

Modularity

A

degree to which a system’s components may be separated and recombined.
allows for building new things using components from something else.
one module can be improved without interfering with the working of the others.
facilitates genetic engineering
examples:
genes=genetic modules, proteins=functional modules
transcription factor binding site
protein domains
operons

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32
Q

How do sigma factors enable modular transcriptional control?

A

by evolving expression of sigma factors, bacteria can evolve regulation of complex functions involving many genes.

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33
Q

Redundancy

A

mechanism of evolvability
its hard to evolve a system where every part is already essential–easier if parts complement each other functionally so that individual parts are not essential.
essential enzymes can make identical copies to create redundancy–leads to evolution of gene families

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34
Q

cryptic diversity

A

same phenotype, different genotypes

can accumulate in a population which would give it mutational access to a variety of new phenotypes.

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35
Q

population genetics

A

studies quantitatively genetic diversity within populations and the mechanisms through which it changes over time.
example research questions: How long does it take for a mutation to fix?/What genes were under selection in humans but not in chimps?
useful for extracting evolutionary information from sequence data
here, evolution=change in the distribution of alleles in a population

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36
Q

genetic drift

A

evolution with out natural selection or mutation.
every individual has equal number of children and survival is random, results in a changed distribution of alleles.
relative abundance of different alleles in a population changes across generations
depends on population size (N) but population that is considered is smaller than actual size because not every individual leaves offspring.

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37
Q

demographic shift

A

population size fluctuates due to the random nature of birth and death processes

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38
Q

frequency of neutral alleles naturally fluctuates over time

A

fluctuations decrease when population size (N) increases.

100-fold increase in size decreases fluctuations 10-fold

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39
Q

what is the probability that a neutral allele will become fixed in a population?

A

equal to the initial frequency of that allele.

40
Q

diversity generally decreases over time. WHY?

A

drift leads to gradual loss of allele diversity

generally -1/N is the fraction of diversity lost in one generation. N=population size.

41
Q

Ne

A

effective population size-fraction of population that leaves offspring.
number that captures genetic drift of population
determines fates of beneficial and deleterious mutations in a population.
effective population size is dominated by the smallest size.
rate of diversity loss due to genetic drift is actually 1/Ne

42
Q

bottlenecks

A

occur when population size temporarily decreases.
increases impact of genetic drift
leads to reduced genetic variation

43
Q

founder events

A

occur when a few members of an original population start a new population.
increases impact of genetic drift.
examples: ancient humans leaving Africa-only a select few traits left/survived. Afrikaner population in South Africa has high rate of Huntington’s because original Dutchies happened to carry gene at high frequency.

44
Q

Neutral theory of molecular evolution

A

at molecular level majority of DNA variants in most populations are selectively neutral.
neutral variants accumulate through genetic drift rather than natural selection.
many lethal mutation, more nearly neutral/neutral mutations, few beneficial ones.

45
Q

sources of neutral variation at the DNA level

A

degeneracy of genetic code
amino acid substitutions that do not affect protein structure.
non-coding regions

46
Q

nucleotide substitution

A

two divergent populations will accumulate differences through this process
happens when a novel allele arising through mutation increases to fixation in one of the populations
rate of accumulation is independent of population size=constant rate=molecular clock
(rate mutations emerge uN)X(1/population size N)=u

47
Q

the molecular clock

A

substitutions accrue over time
for many genes the rate of neutral substitutions is clock-like: a roughly constant rate of ticking as substitutions take place.
function of gene presumably remains the same, neutral substitutions accumulate.
differences in DNA sequences between two species are proportional to the time elapsed since the divergence from their most recent common ancestor.
**different genes have different clock rates.

48
Q

human mitochondrial molecular clock

A

clock calibrated to setting Human-chimp split to 6.5 millions years.
shows that Africans are more diverse=origin of human life and that Europeans/Asians are from a smaller, more recently diverging gene pool
used mitochondrial DNA because mitochondria comes from mother, reduces complications of parents from mixed lineages, similar to asexual replication.
rate of mitochondrial mutation is calibrated to a fast clock, appropriate for studying such a short time period.
also practically it was easier to sequences the shorter sequence of the mitochondria by SAnger than a different human gene.

49
Q

Did polio spread HIV?

A

No.

Based on molecular clock, HIV was diversifying since the 1930s and polio vaccines were only used starting in the 1980s.

50
Q

McDonald-Kreitman Test (MK test)

A

tests of positive selection-answers if a gene has been accumulating multiple beneficial mutations over time.
compares polymorphisms and divergence for synonymous and non-synonymous changes.
requires sequence of a coding gene in at least two species and polymorphism data (variants in the population) for at least one individual.

51
Q

synonymous vs. non-synonymous

A

synonymous=do not change the amino acid. expected to be neutral mutations.
non-synonymous=missense mutations. change amino acid. expected to be deleterious or neutral but some could be beneficial.

52
Q

divergence vs. polymorphism

A

divergence: mutations becomes fixed in a population
polymorphism: mutation is not fixed; only some members of population have it.

53
Q

setting up MK test

A 
make a 2x2 contingency table. 
Dn=fixed, non-syn
Ds=fixed, syn
Pn=polymorphic, non-syn
Ps=polymorphic, syn
54
Q

if Pn/Ps>Dn/Ds then

A
  1. there are stable polymorphisms coming from heterozygote advantage.
    Pn is high and Dn is low because mutations do not fix
  2. weakly deleterious mutations that are not cleared effectively by selection. never fix
  3. recessive deleterious mutations. one defective copy is ok but two is lethal. hard to clear because recessive phenotype is unlikely when recessive gene is rare.
55
Q

if Dn/Ds>Pn/Ps then

A

accumulation of beneficial mutations=positive selection

**beneficial mutations tend to become fixed quickly, increasing Dn and decreasing Pn

56
Q

if Dn/Ds=Pn/Ps then

A

mutations are either neutral or strongly deleterious===the null hypothesis of MK test and expected if a gene is conserved.

57
Q

statistical significance of MK test

A

generally, Dn/Ds=/=Pn/Ps
can use a FIsher exact test to determine if difference between two columns of contingency table is significant.
p-value of 0.01 means that we reject the null hypothesis with 99% confidence.

58
Q

selective sweep

A

elimination of diversity from a population as a result of a beneficial mutation increasing in frequency.
basically genetic hitchhiking.
if an asexual microbial population has very low diversity this might be indicative of a recent selective sweep in the population.

59
Q

selective sweep

A

elimination of diversity resulting from a beneficial mutation increasing in frequency
if an asexual population has low diveristy compared to what is expected from neutral theory, this might indicate a recent selective sweep

60
Q

signature of selective sweep with recombination

A

diversity is only lost near the beneficial mutation
reduced nucleotide diveristy near a selected locus
wider region indicated faster sweep/stronger selection

61
Q

selection coefficient

A

alleles can have different contributions to the fitness of organisms
characterizes the fitness effects of an allele relative to the population average
beneficial allele: s>0
neutral allele: s=0
deleterious allele: s<0

62
Q

probability of fexation

A

depends on Ne and S
mutations are more likely to fix for small Ne
if Ne is small, deleterious mutations can fix, esp slightly deleterious ones.
beneficial mutations are not gauranteed fixation

63
Q

Muller’s ratchet

A

in a small asexual population, the fitness of individuals can keep getting stochastically lost from a population with an accumulation of slightly deleterious mutations.
relevant for evolution of intracellular bacterial endosymbionts, mitochondrial DNA, and Y chromosome
sex/recombination can counter the ratchet by continuously creating individuals without deleterious mutations.

64
Q

error catastrophe

A

selection increases frequency of genotypes with the highest fitness; mutations lower it
there is an upper limit to the rate of mutation that can be tolerated-beyond the limit, population cannot compensate the influx of deleterious mutations
too high of rate: every generation will contain more deleterious mutations that the previous=the catastrophe.
can happen in any population size.

65
Q

mutation rate and genome size

A

rate inversely proportional to genome size.
viruses can tolerate higher mutation rates because of small size.
higher eukaryotes must keep high fidelity
rationale: keeping mutation rate low is costly/ability to evolve quickly is favored, mutation rate will be below but close to catastrophe threshold.

66
Q

phenotype switching

A

cells existing in different states despite being clones.
isogenic bacteria can switch between different phenotypes in the same environment
phenotypes are reversible and not heritable over generations.
leads to heterogeneity within populations
evolved so that populations can be prepared for changes in environment
can lead to specialization/division of labor in a colony.

67
Q

resistance vs persistance at mechanistic level

A

resistant bacteria are genomically different from sensitive bacteria; a result of natural selection and mutation
Persistence: cell is in different state than non-persistent cell. they all still have same genomic information

68
Q

do persisters arise in response to an exposure to antibiotics or do they pre-exist?

A

microfluidic experiment showed that persisters pre-exist when population is treated with antibiotics.

69
Q

phenotypic switching and bet hedging

A

microbial community can make sure that at least some individuals survive no matter how the environment fluctuates by maintaining individuals with diverse phenotypes.

70
Q

fast-switching vs slow-switching phenotypes

A

fast-switching favored when environment changes fluctuates rapidly.
slow-switching favored when environment rarely changes.

71
Q

when is phenotypics switching preferable to environmental sensing?

A

it can be too late to respond to a change in the environment after it happens (exposure to antibiotics)
too costly to continuously monitor the environment or maintain machinery for responding to rare events
suitable environmental cues might be unavailable.
maybe impossible to know what is best
kill the winner dynamics can favor rare phenotypes.

72
Q

specializations of B. subtilis

A 
surfactin producer
competent to uptake environmental DNA
motile 
dead to feed non-sporulating cells/provide DNA to competent cells
spore
cannibal
biofilm former
miner
73
Q

types of stochastic phenotypic variability

A

state switching: random in occurence and time at each state
excitability: in other state for specific amount of time
Procrastination: stochastic delay in commitment to next stage.

74
Q

biological species concept

A

species are groups of interbreeding natural populations that are reproductively isolated from other such groups.
not a species if organisms do not mate regularily in nature or mattings result in infertile offspring.
species are genetically independent
population genetics can be applied to each species separately

75
Q

pre-mating isolation

A

potential mates don’t meet because of different habitats or mating season
potential mates don’t mate but meet because of different behavior or different pollinators in plants.
ex: coral polyps release gametes at different times.

76
Q

postmating, prezygotic barrier

A

try to mate but can’t form a zygote

incompatible genitalia or gametes

77
Q

postzygotic isolation

A

hybrids formed but have low fitness either because they are sterile or die or because they dont fit a niche or have inappropriate mating behavior.
ex: horse and donkey make mule but its sterile.

78
Q

what are the factors limiting the formation of new species?/what makes speciation hard?

A

need strong selective pressure to cause speciation
need multiple individuals to establish new species not just a single mutant
2 species have to avoid competitive exclusion

79
Q

allopatric speciation

A

populations evolve reproductive barriers in geographic isolation

dispersal: few individuals colonize an isolated area
vicariance: physical barrier forms splitting up species.

80
Q

sympatric speciation

A

speciation occurs within a freely interbreeding population

81
Q

mechanisms of allopatric speciation

A

gene flow interrupted by geographic barrier
variant types appear
drift/different selection pressures cause divergence between isolated gene pools
reproductive isolation is present even if geographic barrier is removed.

82
Q

examples of allopatric speciation

A

formation of Panama Isthmus separated marine organisms
Congo River separates chimpanzees and Bonobos
grand canyon separated two types of squirrels.

83
Q

examples of sympatric speciation

A

cichlids in Lake Victoria

84
Q

mechanisms of sympatric speciation

A

disruptive/divergent selection on a phenotype
and individuals must mate assortatively with other of similar phenotype.
flys that feed on red or green apples do not mate with eachother
**sex and recombination try to oppose this process
chromosome changes can act as barriers to gene flow and facilitate sympatric sepeciation

85
Q

Are there bacterial species?

A

case study:

non-pathogenic, uropathogenic, enterohaemorrhagic E. coli sequenced and compared. Only .39.2% of genomes were similar

86
Q

phenetic species concept

A

define taxonomic clusters based on on similarity of phenotypic characters such as cellular morphology and compposition, growth requirements and other metabolic traits.
traditional approach before sequencing
requires isolation and culturing
morphology also only way to classify fossils of extinct stuff

87
Q

phylogenetic species concept

A

defines species as monophyletic groups of evolutionary closely related individuals
OTUs used in microbiology
<1% difference is 16s rRNA, >70% DNA hybridization efficiency
natural phylogenetic clusters might not exist, making similarity cutoffs arbitrary
can be applied to sexual and asexual organisms but HGT a problem

88
Q

ecological species concept (ecotypes)

A

group of organisms adapted to the same ecological niche
competitive exclusion/selective sweeps an lead to high genetic similarity-leading to congruence between ecological and phylogenetic clusters
if there is recombination, sweeps might not purge diversity of entire chromosomes
problematic if strains can readily change ecotypes through mutations/HGT

89
Q

biological species concept

A

can potentially be applied to/useful for groups of bacteria with high reates of homologous recombination
for bacteria: define species as populations that have high rates of recombination within the populations but low rates of recombination between the populations.

90
Q

multi-locus sequence typing (MLST)

A

genes of a core genome are sequenced and compared.

used to construct trees for closely related strains and define species

91
Q

define ecotype

A

groups of organisms that occupy the same ecological niche
diversity is periodically purged by selective sweeps, making organisms in the ecotype similar to eachother and different from other ecotypes
HGT might help bacteria switch ecotypes
bacteria that occupy different ecotypes can have almost identical genotypes

92
Q

non-homologous recombination vs homologous recombination

A

non-homo: new DNA from donor cell is incorporated into existed DNA of transformed cell
homo: new DNA replaces similar region in recipient organisms

93
Q

homologous recombination

A

aquisition of a foreign pice of DNA and replacement of an existing region in the genome
via DNA uptake from the environment, plasmid conjugation, viruses packing bacterial DNA
rate of homo recom decreases with the sequence difference.
analog to sex in bacteria
raises possibility of using the biological species concept for at least some groups of bacteria

94
Q

is the evolutionary history of different loci/genes the same?

A

yes if clonal; consistent/congruent trees for different MLST loci indicates clonal evolution
no if recombining; inconsistent/non-congruent trees for different loci indicate homologous recombination is important
phylogenetic species concept is problematic

95
Q

coevolution

A

changes in phenotype of one organism can change the selection pressures on other organisms
influence of one species on the evolution of another species depends on the strength and frequency of the ecological interaction

96
Q

diffuse coevolution

A

coevolution in larger webs of less specific interaction

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