EVE 100 MT 1

what is evolution?

- heritable change in populations over time (generations)

- occurs at genetic and phenotypic levels

- a property of populations and NOT individuals

what is adaptive evolution?

this is evolution that causes an organism to be better adapted to their environment, however not all evolution is adaptive. this is an example of a genetic algorithm acting on living organisms

is adaptive evolution random or directed?

neither and both! adaptive evolution has both directional and random aspects to it because it is an algorithmic process!

what is meant by higher fitness?

higher probability of survival and reproduction

what is an algorithm?

it is (in simple terms) a set of steps used to solve a problem or receive a certain output.

what exactly does an algorithm test?

it only tests how well things work, it does not test how things work

what is a single elimination tournament?

this is the same structure as a sports tournament, two individuals will be compared on their ability to perform a task and then the best will compete against each other until one single individual is left

what are the properties of algorithmic processes?

- the algorithm itself is the specific type of steps used to yield the desired output

-an algorithmic input is the specific individuals the the algorithm is being enacted on (sports teams, boxers, dogs in a race, etc.)

- a fitness function or optimality criterion is the thing that you are testing each input on (winning a game, beating another boxer, being the fastest and winning the race)

what is the difference between deterministic and stochastic algorithms?

- a deterministic algorithm is one where the algorithm could repeat many times over and you will still get the same result

- a stochastic algorithm is one where a random variable in the algorithm decreases the predictability of the algorithm, each round might yield a different result. (ex. russian roulette)

how can automated algorithms convert random input into directional change?

automated algorithms can do this by changing the optimality criterion, what exactly are these individuals being chosen for?

is natural selection stochastic or deterministic?

it is stochastic!

what are genetic algorithms, and how do they work?

this is a type of algorithm where you:

- input a random population

- you test them for a specific fixed optimality criterion and select those which are the "best"

- then you replicate them in large numbers

- introduce random changes into some of the copies and leaving some unchanged

- repeat the algorithm many times

can a genetic algorithm operate in the biological world? what will be the outcome of such an algorithm? can it produce anything useful/novel/complex?

genetic algorithms cannot know what the end goal is, but the output can yield novel and useful designs

they can produce software, material design, be used in mechanical engineering, etc.

in biology, biological evolution is a typical genetic algorithm, when our DNA is replicated, random mutations or recombination can induce changes that will allow us to be tested and selected for maximal survival and reproduction probability (natural selection)

how did Darwin describe the first genetic algorithm without knowing what an algorithm was?

he coined the term natural selection as he observed it in organisms he studied, and this description was a typical genetic algorithm since natural selection is a genetic algorithm

what is a linear algorithm?

this is when a process is done once through to reach a certain output or goal

what is a cyclical algorithm?

this is when a process is done many times over to reach a certain output or goal

what conditions must all be met for evolution to occur?

1. variation must be present

2. variation must be heritable

3. variation must affect the probability of survival and reproduction

4. new variation must be generated

how can we compare different populations when traits vary both within and between populations? what can we infer from the differences between trait distributions?

a small difference in means can make a large difference at the tails of a trait's distribution, these are the best places to compare traits which vary within and between populations

what happens when traits depend on a combination of many different factors? what does it mean for some factor to be predictive of trait values?

the variability in traits between populations can be due to a variety of variables, and each variable will only be predictive for a fraction of he overall variation

How can we determine whether a phenotypic trait is heritable? what does it mean to be heritable? what are strongly vs weakly heritable traits? can highly heritable traits still be affected by environment?

we can look at differing genotypes in identical environmental conditions (this is called a twin study), measuring very large samples. this can help attribute any differences to the heritability or the genetics of the trait. strongly heritable(h = 1) traits play a large role in population variability, while weakly heritable (h = 0) traits play a small role

heritability refers to the likelihood of responding to selection

yes!! a large majority of genes are affected by both genetic variability and environmental variability

what is the breeder's equation?

this is R = (h^2)S

- R = the difference between the mean of the parents before selection and the mean of the offspring (response to selection)

- h^2 = scaling factor, can be estimated

- S = the difference between the mean of the population and the mean of the individuals that reproduce

what are reaction norms?

- a reaction norm is the reaction of a given genotype to different conditions (phenotypes produced in different environments) - seen as a line on the graph

what are shared environmental effects?

this is represented by C^2, which is the environmental factors that make family members or siblings resemble each other or be similar to each other

what is a non-plastic trait?

a given genotype produces the same phenotype in any environment, these traits only have genetic variation (no environmental)

what is a plastic trait?

a given genotype will produce different phenotypes as the environment changes, these can have both genetic and environmental variation

what is a genotype-environment interaction (G*E)?

this is when different genotypes respond differently to the same changes in the environment and will each have different reaction norms

one genotype could increase in fitness while another decreases in fitness

how much variation is there at the molecular level? where does it come from?

on average, humans vary by around 2.5 million nucleotide substitutions - this is a lot!!

these genetic differences exist because humans reproduce sexually, recombination plays a significant role because each individual will be genetically unique

molecular variation can arise from changes at the level of protein structure or gene expression and affect phenotypes

the raw material for evolution is unlimited!

what is meant by "nucleotide diversity"?

this is the average proportion of nucleotides that differ between two randomly chosen sequences in a population

does genetic variation affect fitness?

the probability of survival and reproduction is what we call fitness:

- this is a property of genotypes, not individuals

- natural selection is stochastic, fitness is a probability and not a guarantee

- fitness is relative to your population

yes! genetic variation can directly affect fitness of individuals, examples such as birth weight and fertility

if natural selection always acts to increase fitness, then why do we see any natural variation for fitness at all? why doesn't selection maximize everyone's fitness?

the optimal genotype is different in different environments, environmental variation will maintain genetic variation for fitness

this variation has a very large genetic component which allows adaptive evolution to be possible

fitness is relative, there is no such thing as the absolute most fit since each environment will have different fitness levels

not all traits can be maximized to be the most fit because there is a limit of time and energy available, must make trade offs!

what are fitness trade-offs, and how do they affect variation in nature?

this is where an individual can have different variables which may counteract each other and change individual fitness in interchangeable ways

example is the newt given in class; these newts produce tetrodotoxins (TTX). if they produce large amounts of TTX, they are less likely to be eaten but they cannot produce as much offspring. inversely, if they produce less TTX, they will produce more offspring but they are more likely to be eaten

what are typical mutation rates?

in nature, mutation rates can be calculated per base, per replication event

so it's about 10^-10 ~ 10^-11 (one in 10 ~ 10 million) in cellular organisms

unicellular organisms have much higher mutation rates

per genome per generation: 0.001 ~ 10 or more (at least 3,840,000,000 new mutations in the human genome over human evolution)

why are there high mutation rates but low levels of genetic divergence between different species?

although there can be many mutations, not necessarily all of them will be beneficial, some might be neutral and make no change or some might be deleterious and cause death of an organism

most new mutations will be deleterious or neutral, most will be eliminated by natural selection or lost by random genetic drift

what is a synonymous nucleotide substitution? how will it affect fitness?

this is when the nucleotide substituted will not change the overall amino acid sequence of the protein, would result in a neutral mutation effect on fitness

what is a frameshift mutation? what affect will it have on fitness?

a frameshift mutation will add a nucleotide and change the reading frame of the protein, which can have deleterious affects on fitness

why do beneficial mutations exist and do they come from selection of a particular trait? or are they fully random?

beneficial mutations do exist, but they are usually <<1% of all mutations

this can be tested using bacteria!! cultivating bacterial colonies with replica-plating allows you to basically duplicate the same bacterial colonies to distinguish between colonies which develop mutations that could be beneficial (one plate has no antibiotic, the other has antibiotic -- identify colonies which grow with the antibiotic as this is an example of a beneficial mutation)

performing this experiment tells us that mutations are random even if they are beneficial, development of antibiotic resistance emerged randomly before introduction to antibiotics! directional evolution is based on random mutations!

what is the principle of the Hardy Weinberg equation?

this mathematical concept states that the frequency of a certain genotype depends fully on the frequencies of the alleles involved. genotype frequencies will not change from generation to generation.

equation: p^2 + 2pq + q^2

what assumptions need to be made for Hardy Weinberg Equilibrium? if they are all met, what happens? why is this model unrealistic?

1. random mating

2. population of infinite size

3. no mutations

4. no immigration or emigration

5. equal viability of genotypes and gametes (no selection)

if these are all met, then:

- allele frequencies will remain constant indefinitely

- genotype frequencies will attain equilibrium after one generation and then remain constant

this means no evolution! so this is used as a null model to study evolution in populations when each condition is not met

what are two violations of the hardy-weinberg equilibrium assumption of random mating? what are they and how do they affect genotype frequencies?

- inbreeding

typically decreases average fitness (this is because most deleterious mutations are recessive); fitness of offspring is inversely proportional to the parents' degree of relatedness; this changed genotype frequencies, since homozygotes are increased

- assortative mating

individuals select mates according to their genotype, because they are similar. this can be positive (more likely to mate with an individual maximally similar to themselves) or negative (more likely to mate with an individual maximally dissimilar to themselves) and can change allele and genotype frequencies. negative AM can increase frequency of heterozygotes, and positive AM would decrease frequency of heterozygotes

how is social homogamy different from assortative mating?

social homogamy is when individuals are more likely to mate because they are more likely to meet (within the same space)

assortative mating is when individuals are more likely to mate because they are similar to each other

what is a violation of the HW equilibrium assumption of population of infinite size?

genetic drift!

there is no such thing as a population of infinite size, finite population sizes will be affected by sampling variance (how much a specific statistic fluctuates between sample sizes). some individuals will not reproduce and others will reproduce more than once, this random variation will lead to random changes in allele frequencies (genetic drift)! in every finite population, allele frequencies will ALWAYS eventually reach fixation (100%/0% or 0%/100%)

how does the variance rate differ between population sizes?

in large populations, variance will increase more slowly.

true or false: genetic diversity is larger in a larger population

true

what is coalescence?

this is a consequence of genetic drift. any allele will have only two possible fates: being lost or becoming fixed at some point in the future. so in any finite population, all gene copies will eventually become identical by descent...in other words: all alleles that are present in the population today are descended from a single ancestral allele, they all coalesce to one single ancestral allele!

what is the probability of fixation of any allele?

this is equal to its current frequency in the population!

p = n (# of alleles) / 2Nₑ

the average coalescence time for autosomal genes is 4Nₑ (4 x population size)

what is the "effective population size"?

The average number of individuals in a population that contribute genes equally to the next generation. Usually smaller than the actual population size

What are bottlenecks and founder events, and how do they affect genetic variation in populations?

this is when severe reductions in population size will dramatically alter the genetic variation of the population, and accelerate genetic drift

what is gene flow? What are the consequences of migration and gene flow for the distribution of genetic variation in nature?

gene flow is a violation of the HW equilibrium assumption of no migration or emigration. it is the exchange of reproducing migrants between populations.

gene flow increases genetic variation within populations, and reduces differentiation among populations

What are the genetic consequences of natural selection? If we know the mode and strength of selection, how can we predict what allele frequencies will be in the future?

the selection of a specific genotype will be multiplied by the genotype frequency and plug them both into HW equilibrium, and this will help calculate the ratio of genotype frequencies after selection.

if the selection for each genotype was the same, then this would be the same as saying there is no selection and this would give the initial HW equilibrium equation

selection causes a change in allele frequencies!!

a deleterious mutation will be eliminated from an infinitely large, randomly mating population faster if it is (full recessive/co-dominant)?

co-dominant

dominant alleles have a large role in selection

What do we need to know in order to predict future allele frequencies?

the selection coefficient, the allele frequencies, genotype selection frequencies, the dominance relationship between alleles

What are these different modes of selection? which are the most common in nature?

- stabilizing

- directional

- balancing

- diversifying

- purifying

- frequency dependent

- directional selection is the selection of a specific trait in one general direction (typically shifting the phenotype frequency one way or another)

- stabilizing is when individuals with traits closest to the population mean will be selected, and progeny phenotype frequency will reflect the population mean and the distribution will become narrower

- diversifying is when a normal distribution will split or disrupt into two different distributions, selection against the typical phenotype in a population

- new mutations are more likely to be harmful, so purifying selection would be selection against new deleterious mutations in a population

- balancing selection maintains many different alleles rather than selecting one and eliminating others

- frequency dependent selection is when the selection of the trait depends on the frequency of the trait - negative/inverse frequency dependent is when the phenotype which has a smaller frequency has higher fitness

the most common modes of selection in nature are stabilizing selection and purifying selection, as these maintain adaptations while weeding out deleterious alleles and reducing genetic variation

what is batesian mimicry? mullerian mimicry?

- batesian mimicry is when edible species mimic inedible species to avoid predation

- mullerian mimicry is when inedible species look similar to each other to collectively avoid predation

What happens when the direction of selection, and the fitness values of alleles, change over time?

adaptive evolution!

which forces act to increase genetic diversity within populations? which forces act to decrease genetic diversity within populaitons?

increase:

- mutations

- balancing selection

- gene flow

decrease:

- genetic drift

- directional selection

- stabilizing selection

which forces cause populations to diverge positively and negatively? (become more or less similar to each other)

positively:

- genetic drift

- directional selection

- disruptive selection

negatively:

- gene flow

- stabilizing selection

which forces will induce local adaptation? which ones will inhibit local adaptation?

induce:

- directional selection

- disruptive selection

inhibit:

- gene flow

- mutation

- genetic drift

What shapes the balance between mutation and selection? What determines the frequencies at which deleterious alleles are found in natural populations?

mutation-selection balance is calculated via the allele frequency equilibrium, which is directly proportional to the mutation rate and inversely proportional to the selection coefficient

(q eq = sqrt[u/s])

How does selection interact with genetic drift? Are there conditions under which genetic drift is more important than natural selection?

these both will affect allele frequencies

when selection coefficient is >> 1/4Ne (effective population size), then selection will predominate

when selection is << 1/4Ne (effective population size), the effects of drift will predominate (more important than selection)

Why do some human populations have surprisingly high frequencies of deleterious alleles?

this is because they have a physical or cultural isolation which has caused founder effects and genetic drift and high frequencies of deleterious alleles

what is Muller's ratchet?

this is where the mean number of mutations per genome goes up from generation to generation, but it can only stay the same or increase, it can never decrease

How does recombination modify the effects of selection on allele frequencies? And why does recombination accelerate adaptive evolution?

DNA recombination provides an escape from Muller's ratchet, different genomes will carry different harmful mutations, and when they recombine they can leave a genome with no harmful mutations

it also breaks the linkages between beneficial and deleterious mutations and uncouples their evolutionary fates

it can also combine multiple beneficial mutations in a single genotype and be more likely to all be selected and fixed

what is genetic hitchhiking?

genes that are physically linked to a positively selected allele will increase in frequency due solely to that linkage

what is a selective sweep?

this is a type of genetic hitchhiking when a beneficial mutation will drag linked neutral mutations to fixation with it

what is background selection?

this is when selection against a harmful mutation will also remove linked neutral polymorphisms

what happens when beneficial and deleterious mutations are linked?

since they are linked, there are only two paths they both can go together, they either both become fixed or they both are selected against, you cannot uncouple them in asexual populations

what is the purpose of phylogenetic analysis?

this is meant to reconstruct past generations to try and understand their population genetics and genetic variations

what are these phylogenetic tree terms?

terminal nodes

internal nodes

branches

root

- a terminal node is the currently existing taxa

- an internal node is the extinct common ancestor of involved taxa

- a branch indicates shared descent, changes depicted on each branch will belong to all individuals following the branch

- the root is a node that indicates the single common ancestor of all individuals on the tree, this whole connection will be considered a "clade"

how can branch length depict evolutionary relationships?

different branch lengths can indicate differences in evolutionary rates between generations, or between individuals at the same time

do phylogenetic trees indicated similarity or relatedness?

these trees indicate relatedness, some organisms may be very similar due to homologous structures but they may not be the most genetically related!!

what does rooting indicate on a phylogenetic tree?

rooting indicates which lineages within the entire clade were the first to diverge, and can also indicate the degree of relatedness for all members of the clade

what is an "outgroup"?

on a phylogenetic tree, the outgroup is an individual which is not belonging to the clade with taxa of interest (for example, humans on a phylogenetic tree of birds), this can help identify the location of a root in a tree

what is a monophyletic taxa?

this is a taxa that includes all descendants from a last common ancestor

what is a polyphyletic taxa?

this is a taxa that includes descendants from different ancestors, one taxa has a different MRCA than the taxa it is being compared to

what is a paraphyletic taxa?

this is a taxa that includes some of the individuals which diverge from the last common ancestor, but not all.

what is a character and a character state?

a character would be the specific position of a nucleotide on a DNA strand (nucleotide 5), however the specific nucleotide that takes that position (C, T, G, or A) would be the character state

another example could be with coat color, coat color is the character and the actual color (brown, green, red) is the character state

what is homology? why is it considered a hierarchal concept?

this is when a character will share common descent, for example they could be derived via evolution from a common ancestral character

what is the difference between a shared derived character and a shared ancestral character?

what is the difference between all five of these characters in a phylogenetic tree?

synapomorphy

symplesiomorphy

apomorphy

plesiomorphy

atapomorphy

homoplasy

- an apomorphy is a character that is derived

- a symplesiomorphy is a character that is shared amongst taxa because it is ancestral

- a synapomorphy refers to a derived character that is shared amongst all taxa belonging to a common ancestor

- a plesiomorphy is a group of taxa that are grouped by their failure to evolve a derived character that is present in other related taxa

- an autapomorphy is a derived character that is unique to one taxon

- a homoplasy is a character that has evolved independently by chance more than once, and does not indicate relatedness in the taxa that both have the character

which characters are the only types that hold genetic information to base evolutionary relationships off of?

synapomorphies!

which parts of a phylogenetic tree are the only parts that we can observe?

the terminal nodes, which are the currently existing taxa

what is parsimony?

this is a phylogenetic and statistical phenomenon that involves reconstructing evolutionary relationships which yield the least amount of character changes over time. for example, a character evolving twice independently on the tree in two distantly related taxa, vs the character evolving once because these two taxa are reorganized to be considered more closely related

is parsimony always followed in nature?

no, there will always be deviations from parsimony in nature because there is no physical or biological law that says all characters will evolve parsimoniously. homoplastic changes are too common and are more important in the reconstruction of phylogenetic trees than parsimony, parsimony really only indicates the most likely evolutionary relationship between characters!

what is parallel evolution?

this is the independent evolution of the same feature in individuals that are closely related or share a recent common ancestor (this could be due to similar ancestral structures)

what is convergent evolution?

this is the independent evolution of the same feature in individuals that are distantly related or relatively unrelated (this could be due to similar environmental pressures)

what is a secondary loss?

this is when a trait may be derived in a specific clade on a phylogenetic tree, and then the trait is lost somewhere in that clade (such as at the terminal node)

which type of molecular sequences are more susceptible to homoplastic changes? DNA or proteins?

DNA sequences are more susceptible to homoplastic change because there are very limited character state changes (4 nucleotides) in the DNA sequence, while proteins have ~20 amino acid possibilities. the probability of chance similarity is very common!

which coding region on a DNA sequence would you expect to be the most susceptible to homoplastic change? codon 1, 2, or 3?

the 3rd codon position, this is because this region of the DNA sequence is considered the "wobble sequence", it is the one which is most likely to cause neutral changes to the protein, in other words it is most likely to have changes which do not change the amino acid being added to the protein due to the redundancy of the genetic code

what is a 'consensus tree'?

this is a type of tree which essentially indicates an uncertainty in the relationship between a group of individuals, instead of a normal bifurcation that shows a relationship with 2 individuals, it might show an even relationship between many individuals at the same node on the tree

how can the difference in genetic rate of evolution cause differences in phylogenetic tree reconstruction?

genes which evolve rapidly can make it really easy to observe recent relationships between organisms

however, slowly evolving genes make it difficult to observe recent relationships and instead have a large role in determining deeply rooted relationships!