Exam 1 Flashcards
when was Hardy-Weinberg equilibrium discovered?
1908
what is the basis of the Hardy-Weinberg equilibrium?
allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences
Hardy-Weinberg is known as evolution’s ___________
null hypothesis
how do we know/determine if a population is at equilibrium?
- determine the gene frequency in the current generation and determine the expected gene frequency for the next generation
- if in equilibrium, there should be no change between the two generations
measures of genotype can predict __________
allele frequencies
measures of allele frequencies can predict _________
genotype
combined probability that two independent events will occur together is equal to the ______ of their probabilities
product
combined probability of two mutually exclusive events will occur is the ________ of their probabilities
sum
getting EITHER heads or tails on a dime is an example of what type of event? how would you calculate this probability?
- mutually exclusive event
- 1/2 + 1/2 = 1
getting heads on a dime and heads on a penny is an example of what type of event? how would you calculate this probability?
- two independent events
- 1/2 x 1/2 = 1/4
what are the 2 conclusions of HW?
- given HW, the allele frequencies in a population will not change, generation after generation.
- given HW, if the allele frequencies are p and q, then the genotype frequencies will be p^2, 2pq and q^2
For HW to occur, there cannot be…
genetic drift, selection, migration or mutation
T / F : genetic drift does not depend on population size
F
populations losing alleles by chance is an example of
genetic drift
__________ is often referred as evolution due to “blind luck”
genetic drift
T / F : genetic drift’s influence is equally strong in smaller and larger populations
F, stronger in smaller sizes
what is the founder effect?
the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population
what is fitness?
the success of an organism at surviving and reproducing and thus contributing offspring to future generations
define migration
movement of alleles between populations
if some genotypes survive and reproduce at higher rates than others….
allele frequencies will change over time
can migration change allele frequencies?
yes!
can migration produce genotype frequencies that are not consistent with HW?
yes!
what is an example of migration counteracting selection that we talked about?
allele for banded pattern in snakes is not selected out of island populations even though un-banded pattern is more advantageous to the island snakes
migration can prevent ________
divergence
migration leads to ________ between populations
homogenization
match result to mechanism! (mechanisms: HW equilibrium, genetic drift, natural selection, migration, mutation)
result:
1. a certain allele is lost
2. a certain allele enters a population
3. allele frequencies do not change
4. a new genetic variant appears in the population
5. a certain allele becomes less common
- genetic drift
- migration
- HW equilibrium
- mutation
- natural selection
The frequency of two alleles in a gene pool is 0.22 (A) and 0.78(a). Assume that the population is in Hardy-Weinberg equilibrium.
(a) Calculate the percentage of heterozygous individuals in the population.
(b) Calculate the percentage of homozygous recessives in the population.
(a) 2 x 0.22 x 0.78 = 0.34 = 34%
(b) 0.78 x 0.78 = 0.61 = 61%
there will be no change in allele frequency if…..
selection is not strong enough and/or initial frequency is not high enough
natural selection results in what type(s) of mutations?
adaptive/advantageous
define adaptations
evolutionary modifications that improve the chances of survival and reproductive success
define natural selection
the mechanism by which better adapted organisms are more likely to survive and become the parents of the next generation
population genetics and natural selection combine to explain _____ and _____ evolution
micro and macro
what are 4 impacts of Darwin’s work?
- gave a single explanation to many separate observations
- provided a dynamic view of species
- showed that man was no longer the pinnacle of life
- classification of organisms along evolutionary lines
what are the two central unifying themes of biology?
- all existing organisms are modified descendants of other organisms (common ancestry)
- natural selection - differential survivorship and reproduction is the main mechanism of evolutionary change
describe the usefulness of stratigraphic columns
can age a fossil based on its location in a formation (older if found deeper down)
describe the usefulness of radiometric dating
can age a fossil due to isotopes decaying at a constant rate
what is considered the main evidence for evolution having occurred?
fossils!
what serves as evidence of evolution in living organisms?
morphology, specifically vestigial structures
what are vestigial structures?
reduced or useless body parts that are evidence of evolution
are vestigial structures evidence of macro or micro evolution?
both!
what are some examples of vestigial strucutres?
- “limbs” in snakes
- tiny wings on the flightless kiwi
- tailbone in human
- pelvis in dolphins and whales
contrast macro and micro evolution
- microevolution refers to small changes over short periods of time within a population
- macroevolution refers to larger changes over a much longer time scale
define homology
similarities due to shared common ancestor
describe the homology of bird wings and bat wings - what are they homologous as?
homologous as forearms, not as wings (because common ancestor did not have wings!)
homologous traits are evidence of
evolution!
define analogy
structures/traits that are similar in function but evolved independently
are the similar structures on a whale and a shark analogous or homologous?
analogous (convergent evolution, did not receive traits from a common ancestor)
define/describe developmental homologies
embryos from different vertebrates are very similar early in development
what are some examples of developmental homologies?
gill pouches and postnatal tails
how is the genetic code evidence of homology?
the same nucleotide triplets or codons specify the same amino acid across almost all organisms
_________ are also another molecular homology that serve as evidence for homology
pseudogenes
T / F : the older the pseudogene is, the more mutations it has
T
how can we determine relation amongst organisms through pseudogene analysis?
can determine if they have a pseudogene in common and if the pseudogene has a lot of mutations, then we know that they have been related for a long time
T / F : similar species are often clustered geographically
T
describe how the deep-sea vent invertebrates that we talked about in class are an example of evolution and biogeography
the organisms that are in the same deep-sea vent are more closely related to each other
define suboptimal design
“accidents” of evolutionary history explain many features that no intelligent engineer would be expected to design
what are some examples of suboptimal design?
- human eye has a blind spot
- food and air crosses in the pharynx of terrestrial vertebrates (why you can choke)
can we watch evolution happening?
yes!
did Darwin believe we could see evolution happening?
no :(
what are some examples of evolutionary changes that we can see happening?
- can see adaptations that organisms are evolving due to human impositions on the planet
- ex: beak length of bugs having to grow in order to get food out of balloon vine fruit
the formation of new species is considered ______evolution
macro
variations within a species is considered ______evolution
micro
what are the postulates of evolution by natural selection?
- individuals within populations vary
- some of the variation is passed on from parents to offspring (through genes)
- in every generation, some individuals are more successful at surviving and reproducing than others
- survival and reproduction are not random, but tied to variation
what is the main “unit” of selection?
the individual
the consequences of selection occur and are measured in __________
populations
how do new traits evolve?
natural selection acts on existing variation (ex: more finches with large beaks arose because there were already finches with large beaks)
natural selection acts on ________ but evolution consists of changes in ___________
phenotypes, allele frequencies
what is an example of co-opting existing traits for new functions?
- the panda’s thumb
- the radial sesamoid bone evolved into a “thumb” as it was beneficial for gripping bamboo
is a panda’s thumb homologous to the thumb of a human? why or why not?
no, it did not come from the same bone
what is inductive reasoning?
a summary of a series of specific observations that lead to a general explanation
what is deductive reasoning?
using general explanations to make specific statements
the classical model of science was based on
induction
what was the “basic tragedy” of the classical model based on induction?
there were certainties that scientists thought they would eventually come to based off of their observations but their observations did not prove these assumed truths
what were the problems with the classical model?
- lack of precision
- unexamined alternatives
- data was theory laden
if you are too credulous…
you accept a hypothesis that is false
in basic science, is it better to be too credulous or too skeptical?
too skeptical
if you are too skeptical…
you reject a hypothesis that is true
say a pesticide is being used to prevent a pest from destroying crops, but there is a hypothesis that the crop is harmful to humans!
assess two ways of making a mistake in your decision. what are the consequences? which mistake is worse? how much evidence is needed before the use of the pesticide?
- accept the hypothesis and it is false (too credulous). this leads to the crops getting eaten by the pests
- reject and it is true (too skeptical). it is used on the crops and people get sick
- worse mistake: kind of a value decision
- evidence needed: 95% sure results are not due to chance
why is it better to be too skeptical rather than too credulous?
science often builds on science, and if people are too credulous, work will be built upon false ideas
define phylogeny
a hypothesis about the evolutionary relationships among organisms
define systematics (in terms of evolution)
constructing phylogenetic hypotheses
define taxonomy
the identification and naming of species
what are two things a taxonomist must do in order to reconstruct a phylogenetic tree?
- distinguish between ancestral and derived traits within a lineage (direction of change)
- distinguish between homologies and analogies
why can it be hard to distinguish between homologies and analogies?
divergent evolution may make homologous traits appear dissimilar and convergent evolution may make analogies appear similar
are large ears on rabbits and kangaroos an example of convergent or divergent evolution? homologies or analogies?
convergent, analogies
what are synapomorphies?
shared (due to ancestry) and derived traits
T / F : all homologies are synapomorphies, but not all synapomorphies are homologies
F - all synapomorphies are homologies but not all homologies are synapomorphies
describe shared traits
homologous traits in closely related groups
for derived traits, you need to know…
direction of change (polarity of change)
feathers of fossil birds being structurally similar to feathers of modern birds is an example of a _______ trait
shared
are four limbs in mammals a synapomorphy?
no!
what is a synapomorphy in mammals?
hair
convergence and reversal are both classified as ________
homoplasy
why would sequence data be more susceptible to homoplasy than morphology, for example?
- base pairs can switch and revert, which might lead to outgroups being accidentally mislabeled
- have to look at every single base pair, so if more base pairs are shared/common, more reason to group together
why has it been difficult for scientists to figure out the closest relatives of whales?
whales are very derived
the preferred tree in maximum parsimony is the one that…
minimizes the total amount of evolutionary change
does maximum parsimony assume that synapomorphies or homoplasy is more common?
synapomorphies
what is an advantage of “maximum likelihood” over parsimony when constructing phylogenetic trees from sequence data?
- models of evolutionary change can be considered
- ex: rates at which third base pair in a codon changes can be taken into consideration
- ex: information about different rates in transversions and transitions can be considered
how many possible trees are there for 8 species?
10,395
describe bootstrapping and why it is important
- bootstrapping creates a new data set from an existing data set by resampling and uses this new data set to estimate phylogeny
- it is able to determine how often each branch can be found in the trees estimated from the resampled data
which taxa represents an evolutionary relationship?
monophyletic taxa (taxon 1)
phylogenies can be used to determine _________ and __________
homology, analogy
what is coevolution?
when interactions between species produce adaptations in both
what is cospeciation?
when speciation occurs in two interacting species simultaneously
describe some additional uses of phylogenetic trees
- deciding which flu vaccines to make
- determining which cancer was the initial cancer if a person has multiple types
- determining homologous genes across species
what are the 3 kinds of variation? what is a good example of all 3?
- genetic variation
- environmental variation
- genotype x environment interaction
- ex: skin color
define/describe genetic variation
differences among individuals that are encoded in their DNA
of the 3.5 billion DNA base pairs that make up the human genome, only ____% codes for proteins
1.2
T / F : humans have almost as many pseudogenes as protein coding genes
T
_________ are known as the raw material for evolution and the ultimate source of genetic variation
mutations
define mutations
any change to the genome
what are some mechanisms by which mutations might occur?
- mistake in the copying of DNA
- mutagen (radiation, chemicals, etc.)
- virus
what is the most common type of mutation?
point mutations
describe a transition mutation
purine to purine (A to G) or pyrimidine to pyrimidine (T to C)
transitions occur about ______ as often as transversions
twice
describe a transversion mutation
purines to pyrimidines/pyrimidines to purines (G to C, G to T, A to C, A to T)
transitions and transversions are examples of what type of mutation?
point
what kind of mutation would cause a frameshift?
insertion or deletion
how can a mutation be silent?
if a base pair is changed but the amino acid code is not
nonsynonymous mutations are considered
loss of function
are indels synonymous or nonsynonymous?
nonsynonymous
where do new genes come from?
gene duplication due to unequal crossover
describe promiscuous proteins
proteins capable of carrying out two functions; are especially likely to take on new functions if duplicated
what is a paralog?
a homologous gene that arises by gene duplication
describe gene recruitment
the co-option of a particular gene or network for a totally different function as a result of a mutation; the reorganization of a preexisting regulatory network can be a major evolutionary event
sets of paralogs = __________
gene families
describe gene duplication due to retroposition
- processed mRNA is reverse-transcribed to form dsDNA
- the dsDNA is integrated into one of the main chromosomes, usually resulting in a functionless pseudogene
- can become functional if next to a regulatory sequence or if it acquires one via a transposable element insertion
_________ lock alleles into supergenes
inversions
describe inversions (cause, result, etc.)
- radiation causes two ds breaks in chromosome
- segment detaches, flips and is reannealed
- segments are now locked and cannot be separated by crossing over
T / F : many mutations have little to no effect on fitness
T
can mutation rates evolve?
yes
if mutations are left to accumulate…
can result in reduced fitness
in the C. elegans experiment we discussed in class, why were there more mutations in the line reared in “ideal” conditions?
- more mutations accumulated because nothing was selected out
- everyone was surviving and reproducing, leading to more mutations
novel traits can arise when…
existing genes are expressed in a new developmental context
changes in the expression of developmental genes can dramatically alter __________
phenotypes
what types of genes are often pleiotropic?
genes involved in development
what does it mean for a gene to be pleiotropic?
they have many functions in different cell types
why are mutations in coding regions less common?
more likely to be selected out due to possibility of causing detrimental effects to phenotype
T / F : mutations in coding regions are always detrimental
F, can be detrimental in one context and beneficial in another (pleiotropic effect!)
describe a mutation in a cis-acting element
affect gene expression only in a single developmental context
describe convergent evolution
independent evolution leading to similar traits in two different lineages
are mutations in a cis-acting element or in a coding region more common? why?
in a cis-acting element, less catastrophic effects in the resulting phenotype
convergent evolution is often a result of
similar selection pressures
what is deep homology?
when growth and development of traits in different lineages result from underlying mechanisms inherited from a common ancestor
is the fly eye homologous to the mouse eye, or is it convergent?
both, depending on the level of development examined
a mutation can give us a new species through ________
polyploidy
describe how polyploidy results in speciation
- an “accident” occurs during meiosis
- mutated organism now cannot interbreed with “normal” organism, leading to new species!
what was an example of polyploidy that we talked about in class?
the spotted salamander
how do scientists today measure genetic variation in natural populations?
via whole genome sequence
describe ways in which the link between genotype and phenotype can be complex?
- there are dominant and recessive alleles
- multiple genes can influence a single trait
- the environment can influence gene expression
what determines if a variation can evolve?
if it has a genetic component
describe/define phenotypic plasticity
the ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions
what is epigenetics?
the study of inherited changes in phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence
which of the following is NOT true about Charles Darwin?
- he was originally going to be a minister
- his book the “Origin of Species” was almost “scooped” by Alfred Wallace
- he made numerous field trips and observations on these trips led to the theory of evolution
- he had a theory about how traits were inherited that has been demonstrated to be incorrect
he made numerous field trips and observations on these trips led to the theory of evolution
which of the following statements about evolution are true?
- evolution by natural selection has never been clearly demonstrated
- evolution is the change in frequency of alleles over time
- transition fossils are evidence of macroevolution
- while there is evidence for macroevolution, there is very little evidence that supports microevolution
- both 2 and 3 are true
both 2 and 3 are true
which of the following is NOT an example of a homology?
- wings on bats and flippers on dolphins
- dog’s eyes and human’s eyes
- the long ears on a N. American rabbit and the long ears on a kangaroo
- three base pairs that code for the amino acid arginine in insects and the the three base pairs that code for arginine in humans
the long ears on a N. American rabbit and the long ears on a kangaroo
in what way is artificial selection different from natural selection?
- populations do not really “evolve” due to artificial selection
- variation is not passed down from parent to offspring under artificial selection
- all individuals reproduce equally under artificial selection
- humans, not nature, select who will reproduce under artificial selection
humans, not nature, select who will reproduce under artificial selection
which of the following would be an example of making the mistake of being too credulous and the consequence in this case?
- you reject the hypothesis and it is true, so people get sick from use of the chemical.
- you reject the hypothesis and it is false, so people get sick from use of the chemical.
- you accept the hypothesis and it is false, so crops get eaten by pests.
- you accept the hypothesis and it is true so people get sick from use of the chemical.
you accept the hypothesis and it is false, so crops get eaten by pests.
which mistake does basic science try to AVOID and why?
- being too skeptical, because otherwise science would develop too slowly.
- being too credulous, because science progresses by accepting as many hypotheses as possible.
- being too skeptical, because science is so expensive.
- being too credulous, because science does not want to build on false ideas.
being too credulous, because science does not want to build on false ideas.
DNA sequence data has more homoplasies than other kinds of data. which of the following do you think might explain why?
- because it is easier to mistakenly assume that two morphological characters are homologous than two DNA base-pairs.
- because there are only four states to switch between in sequence data, and often numerous states in morphology.
- because DNA sequence data evolves much slower than morphological data.
- because DNA sequence data is more difficult to compare than other kinds of data.
because there are only four states to switch between in sequence data, and often numerous states in morphology.
which of the following would help to identify a trait that has phylogenetic information?
- it has a different state in every single taxa
- it has the same state in all of the taxa
- it is not the same state in all of the taxa
it is not the same state in all of the taxa
which of the following is NOT true about the difference between “basic” and “applied” science?
- applied science takes information that exists and utilizes it to solve and existing problem.
- basic science is primarily concerned with how the information they create might be used.
- applied science relies on the discoveries of basic science.
- all scientific disciplines (e.g. physics, chemistry, biology) can have basic and applied aspects.
basic science is primarily concerned with how the information they create might be used.
which of the following helps explain how there can be “silent” mutations?
- redundancy in the genetic code.
- mRNA does not always function.
- mutations are often insertions of bases.
- each amino acid is coded by a very specific codon.
redundancy in the genetic code
why were there fewer mutations in the control line of the round worm experiment?
- they were not reproducing in the control, so no crossing over.
- natural selection was removing individuals with mutations in the “control” line.
- the researchers controlled for mutations by keeping them under UV light.
- mutations do not occur if the individuals are well fed
natural selection was removing individuals with mutations in the “control” line
which of the following is NOT evidence that the gene FGF4 (produces chondroplasia in dogs) is a duplicate of fibroblast growth factor 4 that arose by retroposition?
- FGF4 and growth factor gene have similar sequences
- FGF4 is located next to growth factor gene
- FGF4 has no introns
FGF4 is located next to growth factor gene
which of the following statements about gene expression is true?
- the environment can influence gene expression thereby altering an organism’s phenotype.
- environmental variation can produce non-genetic inheritance (epigenetics).
- the way your genes respond to the environment can evolve.
- all of the above are true
all of the above are true
which of the following is true about negative frequency dependent selection?
- the more common a phenotype, the higher its relatively reproductive success
- the relative fitness of a phenotype changes based on its frequency
- the two phenotypes will be at frequencies of 50/50 at equilibrium
- while frequencies of the phenotypes change, relative fitness of each phenotype does not
the relative fitness of a phenotype changes based on its frequency
which of the following statements is NOT true about genetic drift?
- genetic drift is a mechanism of evolution
- genetic drift is random
- genetic drift is more common in large populations
- genetic drift reduces genetic diversity
genetic drift is more common in large populations
which of the following would indicate genetic drift?
- loss of heterozygosity within populations with different alleles fixed in each population
- loss of homozygosity with same alleles fixed in each population
- loss of heterozygosity across populations with same alleles fixed in each population
- increased heterozygosity within populations with random alleles being lost in each population
loss of heterozygosity within populations with different alleles fixed in each population
which of the following is true about HW equilibrium?
- when a population is at HW for a gene with two alleles, the frequency of the alleles will be 50/50
- sexual reproduction alone can lead to a population not being at HW for a gene
- HW is basically the “null hypothesis” for evolution
- populations that go through “bottle necks” are more likely to be at HW
HW is basically the “null hypothesis” for evolution
which of the following would have the highest rate of evolution?
- common dominant allele
- common recessive allele
- mutations that are silent
- rare recessive alleles
- the dominance of an allele does not influence its rate of evolution
common recessive allele
what is the evidence for skin color in humans in relation to each of the four postulates of evolution by natural selection?
- individuals within populations vary: skin pigmentation is highly variable across humans
- the variation can be passed down from parent to offspring: we now know many genes are involved, in addition to environmental influences (gene X environment)
- in every generation, some individuals are more successful at SURVIVING and REPRODUCING than others: does not apply
- survival and reproduction are not random, but tied to variation.
- pigmentation has medical implications, influences
both survival and reproduction- ex: too dark – difficult to produce vitamin D
- ex: too light – mutations due to UV
- pigmentation has medical implications, influences
under what conditions would we predict that evolution by natural selection would lead to a population of all one type of plant (sticky or velvety)?
without negative frequency dependence where one plant does better when it is rare; it could be that one plant type does better whether rare or not, and therefore we would predict selection for that type and loss of the other type
how could migration have been responsible for the continued persistence (maintenance) of the polymorphism (sticky versus velvety) plants?
similar to the example in class with the water snakes, the persistence of one of the types could have been because it was found in a neighboring population, and it was maintained in the population they studied as it migrated in (not due to negative frequency dependent selection)
in the “Herbivore‐mediated negative frequency‐dependent selection” reading, did they detect evidence of genetic drift? and if yes, what was it ?
yes. in two of the populations that went through bottlenecks, there was fixation of one of the morphs
T / F : selection cannot act on rare recessive alleles
T
natural selection is most potent as a mechanism when acting on what type(s) of alleles?
rare dominant alleles and common recessive alleles
in the Mukai and Burdick experiment, why did the frequency of the viable allele go down?
balance between negative selection on homozygotes and positive on heterozygotes maintains lethal allele
what are 4 mechanisms that can maintain genetic diversity?
- dominance
- heterozygote superiority
- mutation/selection balance
- negative frequency dependence
once a mutation arrives, _________ and ________ may act on it
drift, selection
what is the mutation/selection balance?
when the rate at which mutations are being created equals the rate at which they are being selected out of the population
what is the equilibrium frequency formula?
q = õ/s
µ = mutation rate
s = selection coefficient
what maintains the cystic fibrosis mutation at 0.02%?
there is a heterozygotic advantage - carriers of the allele are resistant to typhoid fever
describe/define negative frequency dependent variation
- selection favors rare genotypes
- fitness of phenotypes depend on their frequency in the population
negative frequency dependent selection can maintain two alleles in a population if…
each allele has higher RS when rare
according to negative frequency dependence, as the frequency of the yellow flowers increased, their fitness…
went down
how are rare deleterious mutations often brought together?
inbreeding
inbreeding increases the percentage of genetic loci that are _________ for alleles
homozygous
why is inbreeding not considered a direct mechanism for evolution?
because it changes genotype frequencies but not allele frequencies
___________ often go hand in hand with inbreeding and selection if small numbers of individuals establish a new population
genetic bottlenecks
define inbreeding coefficient (F)
the probability that any two alleles at any locus in an individual will be identical due to common descent
what is inbreeding depression?
decreased fitness due to inbreeding
define/describe landscape genetics
a field of research that combines population genetics, landscape ecology, and spatial statistics
define/describe population structure (or population subdivision)
the occurrence of populations that are subdivided by geography, behavior, or other influences that prevent individuals from mixing completely
what would be an indication of genetic drift within populations? among populations?
– within populations: fixed different alleles, loss of heterozygosity
– among populations: chance genetic diversity
define/describe population subdivision
populations that are subdivided by geography (distance between populations) and human made barriers (highways)
population subdivisions can lead to an increase in…
inbreeding
low gene flow is indicative of what two things?
genetic isolation and/or higher inbreeding
