Unit 3 YIPPEE!!!

Question 1

define evolution

Answer 1

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

Question 2

why study evolution?

Answer 2

central organizing principle of biology
human health
technology

Question 3

Lamarckian Theory of Evolution

Answer 3

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

Question 4

Natural selection

Answer 4

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.

Question 5

Luria-Delbruck Experiment 1943

Answer 5

-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.

Question 6

conditions for evolution by natural selection

Answer 6

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

Question 7

adaptation

Answer 7

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

Question 8

outdated adaptation/vestigial structure

Answer 8

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

Question 9

exaptation

Answer 9

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

Question 10

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

Answer 10

genetic drift

genetic draft

Question 11

genetic drift

Answer 11

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

Question 12

hitchhiking/genetic draft

Answer 12

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

Question 13

Fun facts about natural selection

Answer 13

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

Question 14

directional selection

Answer 14

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

Question 15

stabilizing selection

Answer 15

favors average individuals
example: human birth weight
NEED MICROBIAL EXAMPLE

Question 16

disruptive selection

Answer 16

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?!

Question 17

frequency-dependent selection

Answer 17

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

Question 18

negative frequency dependence selection

Answer 18

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.

Question 19

positive frequency dependent selection

Answer 19

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.

Question 20

balancing selection

Answer 20

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

Question 21

Antibiotic-producing bacteria in liquid vs in agar

Answer 21

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

Question 22

genotype

Answer 22

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

Question 23

phenotype

Answer 23

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

Question 24

mutation

Answer 24

change in the sequence of a chromosome

Question 25

horizontal gene transfer: Darwinain or Lamarckian?

Answer 25

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

Question 26

CRISPR-cas system evolution

Answer 26

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.

Question 27

evolution proceeds through (2 steps)

Answer 27

1. mutations created by variants | 2. selection eliminating variants unsuited to their environment

Question 28

evolvability

Answer 28

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

Question 29

mechanisms of evolvability (3)

Answer 29

innovation sharing through genetic exchange modularity redundancy

Question 30

innovation sharing through genetic exchange

Answer 30

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

Question 31

Modularity

Answer 31

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

Question 32

How do sigma factors enable modular transcriptional control?

Answer 32

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

Question 33

Redundancy

Answer 33

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

Question 34

cryptic diversity

Answer 34

same phenotype, different genotypes | can accumulate in a population which would give it mutational access to a variety of new phenotypes.

Question 35

population genetics

Answer 35

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

Question 36

genetic drift

Answer 36

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.

Question 37

demographic shift

Answer 37

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

Question 38

frequency of neutral alleles naturally fluctuates over time

Answer 38

fluctuations decrease when population size (N) increases. | 100-fold increase in size decreases fluctuations 10-fold

Question 39

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

Answer 39

equal to the initial frequency of that allele.

Question 40

diversity generally decreases over time. WHY?

Answer 40

drift leads to gradual loss of allele diversity | generally -1/N is the fraction of diversity lost in one generation. N=population size.

Question 41

Ne

Answer 41

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

Question 42

bottlenecks

Answer 42

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

Question 43

founder events

Answer 43

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.

Question 44

Neutral theory of molecular evolution

Answer 44

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.

Question 45

sources of neutral variation at the DNA level

Answer 45

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

Question 46

nucleotide substitution

Answer 46

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

Question 47

the molecular clock

Answer 47

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.

Question 48

human mitochondrial molecular clock

Answer 48

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.

Question 49

Did polio spread HIV?

Answer 49

No. | Based on molecular clock, HIV was diversifying since the 1930s and polio vaccines were only used starting in the 1980s.

Question 50

McDonald-Kreitman Test (MK test)

Answer 50

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.

Question 51

synonymous vs. non-synonymous

Answer 51

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.

Question 52

divergence vs. polymorphism

Answer 52

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

Question 53

setting up MK test

Answer 53

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

Question 54

if Pn/Ps>Dn/Ds then

Answer 54

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.

Question 55

if Dn/Ds>Pn/Ps then

Answer 55

accumulation of beneficial mutations=positive selection | **beneficial mutations tend to become fixed quickly, increasing Dn and decreasing Pn

Question 56

if Dn/Ds=Pn/Ps then

Answer 56

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

Question 57

statistical significance of MK test

Answer 57

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.

Question 58

selective sweep

Answer 58

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.

Question 59

selective sweep

Answer 59

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

Question 60

signature of selective sweep with recombination

Answer 60

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

Question 61

selection coefficient

Answer 61

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

Question 62

probability of fexation

Answer 62

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

Question 63

Muller's ratchet

Answer 63

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.

Question 64

error catastrophe

Answer 64

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.

Question 65

mutation rate and genome size

Answer 65

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.

Question 66

phenotype switching

Answer 66

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.

Question 67

resistance vs persistance at mechanistic level

Answer 67

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

Question 68

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

Answer 68

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

Question 69

phenotypic switching and bet hedging

Answer 69

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

Question 70

fast-switching vs slow-switching phenotypes

Answer 70

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

Question 71

when is phenotypics switching preferable to environmental sensing?

Answer 71

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.

Question 72

specializations of B. subtilis

Answer 72

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

Question 73

types of stochastic phenotypic variability

Answer 73

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.

Question 74

biological species concept

Answer 74

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

Question 75

pre-mating isolation

Answer 75

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.

Question 76

postmating, prezygotic barrier

Answer 76

try to mate but can't form a zygote | incompatible genitalia or gametes

Question 77

postzygotic isolation

Answer 77

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.

Question 78

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

Answer 78

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

Question 79

allopatric speciation

Answer 79

populations evolve reproductive barriers in geographic isolation dispersal: few individuals colonize an isolated area vicariance: physical barrier forms splitting up species.

Question 80

sympatric speciation

Answer 80

speciation occurs within a freely interbreeding population

Question 81

mechanisms of allopatric speciation

Answer 81

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.

Question 82

examples of allopatric speciation

Answer 82

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

Question 83

examples of sympatric speciation

Answer 83

cichlids in Lake Victoria

Question 84

mechanisms of sympatric speciation

Answer 84

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

Question 85

Are there bacterial species?

Answer 85

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

Question 86

phenetic species concept

Answer 86

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

Question 87

phylogenetic species concept

Answer 87

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

Question 88

ecological species concept (ecotypes)

Answer 88

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

Question 89

biological species concept

Answer 89

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.

Question 90

multi-locus sequence typing (MLST)

Answer 90

genes of a core genome are sequenced and compared. | used to construct trees for closely related strains and define species

Question 91

define ecotype

Answer 91

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

Question 92

non-homologous recombination vs homologous recombination

Answer 92

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

Question 93

homologous recombination

Answer 93

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

Question 94

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

Answer 94

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**

Question 95

coevolution

Answer 95

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

Question 96

diffuse coevolution

Answer 96

coevolution in larger webs of less specific interaction