BIO 345 Evolution Prof Maley & Sterner: Exam 1
nonsynonymous mutation
A mutation in a gene that changes the amino acid sequence of the protein that gene encodes. ex: sickle cell anemia
Which condition is most likely to account for a difference between the census population size (total number of individuals) and the effective population size (Ne) in a rapidly growing population of humans?
Individuals take long time to reach sexual maturity.
What tends to happen to new mutations that are: Deleterious
It tends to go extinct quickly
Why is the somatic mutation rate greater than the germline mutation rate?
Somatic mutations cannot be passed to the next generation. Aka disposable soma therapy
What are the 5 forces of evolution?
1. Natural Selection 2. Genetic Drift 3. Mutation 4. Migration 5. Sexual Selection
What are the Fundamental Principles of Biological Evolution? (14) total
1. Phenotype is distinct from genotype 2. all aquired characteristics are not inherited 3. heredity variation based on genes 4. genetic variation arises by random mutation 5. Evolution is the change in the population, not individual 6. Changes in allele freq may/may not be random 7. Natural selection accts for slight & great differences among species 8. Natural selection can alter populations beyond range of variation by changes in allele frequency 9. Populations usually have considerable variation 10. Differences in species evolve by small steps 11. Species are groups of interbreeding or potentially interbreeding individuals that do not exchange genes with other such groups "evolving gene pools" 12. Speciation: the origin of 2 species from a single ancestor, occurs by the genetic differentiation of geographically isolated populations 13. Higher taxa arise by the sequential accumulation of small differences 14. All organisms form a greater tree of life
What is the role of gene flow
1. equalizes allele frequencies (erodes genetic differences between populations. 2. introduces new alleles into a population from another population where they already exist (similiar to mutations role); results from dispersal (movement of individuals and gametes)
Assumptions of Hardy-Weinberg Equilibrium
1. infinite population size 2. no immigration or emigration 3. no selection 4. mutations are negligible 5. random mating
What effects the rate of evolution?
1. mutation rate 2. population size 3. selective coefficients (benefits of a relative allele) 4. generation time (increase reproduction rate increases mutation) 5. heritability
The snow goose (Chen Caerulescens) has both a blue and a white morph. Inheritance is Mendelian: BB and Bb individuals are blue, while bb individuals are white. If 23 geese in a population of 142 are white, and 119 are blue, how many of the blue geese would you expect to be carriers of the b allele (i.e., Bb heterozygotes)?
68
synonymous mutation (silent mutation)
A base pair substitution that does not change the amino acid that a codon normally produces
phylogenetic tree
A branching diagram that represents a hypothesis about the evolutionary history of a group of organisms.
What is an adaptation?
A derived character that conferred higher fitness than the ancestral character state from which it evolved
What is the tree of life?
A family tree of organisms that describes the genealogical relationships among species with a single ancestral species at its base.
What would a founder effect look like? How would it differ from natural selection?
A graph with a founder effect would have big zig zags from that point forward. Natural selection would either go up (if it was favored) or down (unfavored)
Which hypothesis is least likely to explain the rapid evolution of morphological diversity during the Cambrian explosion?
A mass extinction opened up ecological niche space, allowing an evolutionary radiation of animals.
splicing mutation
A mutation altering the normal splicing pattern of a pre-mRNA.
silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created.
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
What is a deleterious mutation?
A mutation that reduces the fitness of an organism
Sickle cell disease results from a nonsynonymous point mutation of the HBB gene, producing an altered beta chain of hemoglobin. Beta thalassemia is caused by a mutation to the same gene, but instead of an altered beta chain, the final protein is absent or incomplete. Which of these mutations is the most probable cause of beta thalassemia in a patient without a family history of the disease?
A nonsynonymous point mutation resulting in a premature stop codon
Discuss criteria or measurements by which you might conclude that a population is better adapted after a certain evolutionary change than before.
A population could be said to be better adapted after a certain evolutionary change than before if the fitness of individuals possessing that new trait is higher than that of individuals without the trait, or higher than that of ancestors without the trait. On a population level, the intrinsic rate of population growth will be greater than it was prior to the adaptation, unless complicated by a force like density-dependent selection. Because fitness is a function of both survival and reproduction, any measure of these two attributes can be used to assess the adaptive quality of an evolved trait.
metapopulation
A set of local populations, among which there may be gene flow and patterns of extinction and recolonization.
Clade
A taxonomic grouping that includes only a single ancestor and all of its descendants.
How does heritability affect the rate of evolution?
A trait w/ no heritability, no correlation with parents has no traction. 10% heritability = 10% correlation offspring + parents. Noise VS gene (low heritability = increased noise decreased gene)
Adaptation
An adaptation is a feature produced by natural selection for its current function. Generally speaking, adaptations are traits or characters that appear to be too well-fitted to their environment to have arisen by chance. That is, they must be the result of selection. Adaptations may involve morphological, physiological or behavioral traits. They arise through the accumulation of a series of small improvements over time
Which organism depends most on high rates of dispersal and migration for survival of its population?
An annual wildflower that colonizes disturbed patches
what is an evolutionary constraint?
Any factor that biases the variation available for selection, slows the rate of adaptive evolution, or prevents a population from attaining the optimal value for a trait
The figure below shows the distribution of beak depth in early 1977 prior to the drought. What change in average beak height do we expect if this trait makes no difference to survival or reproduction during a drought?
Average beak height will decrease, because it is no longer advantageous to have a larger beak.
Many types of antibiotics that were highly effective a few decades ago are not nearly as effective in the present. Which explanation below best fits Darwin's theory of natural selection?
Bacteria have evolved resistance to antibiotics, driven by natural selection.
Early in the origin of life, as it is presently conceived, there was no distinction between genotype and phenotype. What characterizes this distinction, and at what stage of organization may it be said to have come into being?
Because a phenotype is a manifestation of genes that make up a genotype, genes must first exist in order to make this distinction. Our notion of genotypes and phenotypes cannot be said to have come into being until assemblages of molecules that self-replicated did so via coded information (the first "genes"), not just by repeating their structure. Since the first "life" was probably a set of self-replicating molecules without any coding, there could only be phenotype and no genotype.
Given this graph of an allele frequency in a 9 populations, what happened around Gen 100?
Bottleneck
artificial selection/selective breeding
Breeding organisms with specific traits in order to produce offspring with identical traits.
How can cancer sustain this level of mutation?
Cancer does not need everything a normal cell does. The optimal cancer cell just hijacks what it needs.
What are the effects of non-ionizing radiation?
Cataracts (UV, IR and microwave) Skin Cancer (UV). UV can cause the formation of photoproducts (abberant structures w/ additional bonds involving nucleotides). Photoproducts that are not repaired can cause disruption of replication. The gaps left are filled by translesion DNA synthesis which lack proofreading ability and are error prone.
A population has an allele frequency of p = 0.25 , and it receives immigrants at a rate of m = 0.1 from another population whose allele frequency is 0.75
ChangeP = 0.1 (.075 - 0.25) ---> 0.05 old frequency + change p (0.25 + 0.05) = 0.3
What is genetic drift?
Changes in allele frequencies due to chance
Population evolution deals with
Changes in the frequencies of traits in a group of individuals includes processes such as; drift, mutation, migration and sexual selection
Lineage evolution deals with
Changes in the number and variety of genealogically related groups. Includes processes such as; speciation, extinction, convergence, etc.
Uniformitarianism
Charles Lyell's idea that geologic processes have not changed throughout Earth's history. Uniformitarianism allows evolutionary biology to be an experimental science. An example is: Present observations of erosion on a streambank demonstrate how a canyon was formed.
How would you test if genomic instability is an adaptation in cancer?
Check if it evolves independently in many cases (it does). Do a competition experiment between cancer cells where you manipulate the level of genomic instability and see which phenotype tends to win. Measure if the degree of genomic instability (or just presence/absence) is associated with an increase in the reproduction or survival of those cells. Some mechanisms of instability, like loss of TP53, result in a faster cell cycle, and a decrease in apoptosis.
Refer to the figure showing the phylogenetic tree from Charles Darwin's On the Origin of Species. Based on the figure, which statement is false?
Darwin recognized hybridization as an important means of genetic change.
descent with modification
Descent with modification is simply passing traits from parent to offspring, and this concept is one of the fundamental ideas behind Charles Darwin's theory of evolution.
What do you predict will happen to Fst when populations are separated with no migration (and no selection)?
FST will increase to 1 .When there is no migration the inbreeding coefficient rises rapidly resulting in complete fixation and divergence FST =1 . When there is migration FST equals to 0.2. FST= 1/(4Nem+1) where Nem is the number of.migrants Here the number of migrants is zero therefore FST=1
What happens to FST when populations are connected by migration (say 2% chance of migration per organism per generation, N=100 for each population, and no selection)?
FST will increase to near 1. Because migration leads to change in genetic diversity
What do you predict will happen to FST when populations are connected by migration (say 2% chance of migration per organism per generation, and no selection)?
FST will stay moderate, between 0 and 1
T/F: When an allele is common in a very small population, a small advantage (s << 1/Ne) is sufficient for selection for this allele to be stronger than genetic drift
False
Dispersal (propensity, mode, distance, etc.) is a phenotype that can evolve. In what conditions would natural selection favor greater dispersal?
Find better habitat Find food (when food is patchy) Find shelter Escape depleted or polluted environment Escape predators Take advantage of recently cleared habitat (environmental disturbances) - colonizers Find mates Avoid mating with kin (inbreeding depression) Avoid competition with kin Avoid competition with conspecifics (organisms of the same species)
Imagine you're able to control the amount of rainfall on the island in 1977. How would you test if a taller beak confers a fitness benefit during a drought?
First set the rainfall to average or high levels. Then set the rainfall to a very low level. Compare how adults with shorter versus taller beaks survive (or how many offspring they have) . If adults with taller beaks tend to survive (or reproduce more) than adults with shorter beaks, there is a fitness benefit to taller beaks in a drought. Add another year or two onto the study to see if they don't just survive, but produce more viable offspring, which is another key component of fitness!
Which pair of sequences represents a synonymous mutation?
GCU → GCA
founder effect
Genetic drift that occurs when a few individuals become isolated from a larger population and form a new population whose gene pool composition is not reflective of that of the original population. (decreased genetic variation)
Describe genetic linkage
Genetic linkage describes the way in which two genes that are located close to each other on a chromosome are often inherited together. ... These observations led to the concept of genetic linkage, which describes how two genes that are closely associated on the same chromosome are frequently inherited together.
Consider a hypothetical locus with several segregating alleles. The population size is small, mutation is absent, and none of the alleles has a selective advantage. Which of the following is likely to occur after a long period of time (many generations)?
Genetic variation will decline as alleles randomly go extinct.
What is the null model of population genetics?
Hardy-Weinberg
What can we test with the tree of life?
How many times life originated How lineages are related If lineages have fixed natures When groups of lineages appear
Arrange these organisms in the order of their mutation rates per genome, per generation (from highest to lowest)
Human, fruit fly, HIV, bacteria
How does the selection coefficient affect the rate of evolution?
If an allele has increased selection coefficient, it will replace the ones with a smaller effect.
What tends to happen to new mutations that are: Highly beneficial
If it doesn't go extinct quickly, it tends to go to fixation
What tends to happen to new mutations that are: Slightly beneficial
If it doesn't go extinct quickly, it tends to go to fixation
If an allele (e.g. antibiotic resistance) is at 25% frequency in a population, and there is no fitness differences between alleles (e.g., there is no antibiotic in the environment), what is the probability that that allele will go to fixation? Why?
If the allele is at a 25% frequency, it has a 25% chance to go to fixation.
What is MRCA?
In genetic genealogy, the most recent common ancestor (MRCA) of any set of individuals is the most recent individual from which all the people in the group are directly descended. The MRCA of a set of individuals can sometimes be determined by referring to an established pedigree
Do larger populations evolve more quickly or more slowly? Why?
Increase population size = increase rate of evolution Larger gene pool = increased chance of beneficial variation Dampens the effect of drift and emphasizes natural selection
What is most likely to increase rates of gene flow for a benthic (bottom dwelling) marine invertebrate?
Increased lifespan of planktonic larvae
How do we determine if a trait is an adaptation? hypothesis: birds feathers are an adaptation for flight
Is it heritable? If a trait has been shaped by natural selection, it must be genetically encoded — since natural selection cannot act on traits that don't get passed on to offspring. Are feathers heritable? Yes. Baby birds grow up to have feathers like those of their parents. Is it functional? If a trait has been shaped by natural selection for a particular task, it must actually perform that task. Do feathers function to enable flight? In the case of bird flight, the answer is fairly obvious. Birds with feathers are able to fly and birds without feathers would not be able to. Does it increase fitness? If a trait has been shaped by natural selection, it must increase the fitness of the organisms that have it — since natural selection only increases the frequency of traits that increase fitness. Are birds more fit with feathers than without? Yes. Birds without feathers aren't going to leave as many offspring as those with feathers. How did it first evolve? Did the trait arise when the current function arose? Did feathers arise when flying arose? The answer to this is probably no. The closest fossil relatives of birds, two-legged dinosaurs called theropods, appear to have sported feathers but could not fly. Feathers meet three of the necessary requirements to be considered an adaptation for flight, but fail one of them. So the basic form of feathers is probably not an adaptation for flight even though it certainly serves that function now.
What are the effects of ionizing radiation?
It can cause double and single stranded breaks in the DNA backbone through the formation of hyrdroxyl radicals upon radiation exposure. It can also modify bases. It is used to kill microbes, sterilize medical devices and food b/c of its dramatic and nonspecific effect in damaging DNA, proteins and other cellular components.
Imagine a disease sweeps through a population in Hardy-Weinberg equilibrium, and kills all the heterozygous (Aa) individuals, so that the only survivors are homozygous (AA and aa). Suppose Ne = 4,000 and the aa's make up 10% of the population. How many generations will it take for the population to return to HardyWeinberg equilibrium?
It can only take 1 generation to potentially go back to hardy-weinberg under the right conditions.
If a new beneficial, partially dominant allele enters a population, and is not lost to drift, what are the dynamics of its selective sweep (slow/fast start and slow/fast finish)?
It has a fast start and a fast finish
If a new beneficial, dominant allele enters a population, and is not lost to drift, what are the dynamics of its selective sweep (slow/fast start and slow/fast finish)?
It has a fast start and a slow finish
If a new beneficial, recessive allele enters a population, and is not lost to drift, what are the dynamics of its selective sweep (slow/fast start and slow/fast finish)?
It has a slow start and a fast finish
Not all traits are adaptations. Which statement may also explain the evolution of a particular trait?
It may be a necessary consequence of physics or chemistry. It may have evolved by genetic drift, rather than by natural selection. It may have evolved because it was correlated with another trait that conferred an adaptive advantage.
What happens if the frame shift mutation is not a multiple of 3?
It will shift the reading frame of amino acids, every point after the mutation can be changed and nearly all will be non functional.
If the population size is large, will the drift take more or less time to go to fixation or extinction?
Large population = drift takes longer to go to fixation/extinction
Do larger populations evolve more quickly or more slowly? Why?
Large populations may have more mutations but they evolve more slowly due to selection.
In the model, how does the size of the fertility effects of the mutations affect the equilibrium level of fertility in the population?
Larger mutation effects reduce the equilibrium fitness of the population
What are non-adaptive traits?
Learned behaviors (e.g., writing, the two-legged goat) Outcome of genetic drift Correlated features (esp. during development, e.g., male nipple) Historical structures (e.g., human throat arrangement)
Assume the common ancestor at the root lacked a trunk, true leaves, and seeds, and that all evolutionary changes in these traits are shown. Which taxon has a trunk but not true leaves? See image
Lepidodendron
Primary hypothesis: multicellularity evolved many times as shown in the tree below. Alternative hypothesis: New lineages originated independently over time and progressively increased in complexity How is the figure incompatible specifically with the claim that lineages increased in complexity over time?
Many lineages with relatively ancient origins have not evolved multicellularity. For example, the cryptophytes and core jakobids are two taxa that still exist today but have not acquired even intermediate complexity such as colonial life forms. Thus while multicellularity is a recent trait in many groups, it is not strongly correlated with how long ago a lineage started.
What trend would we expect if taller beaks enable G. fortis to eat harder seeds? Choose the trend that best matches your hypothesis.
Maximum seed hardness should increase with beak height
Why is migration important?
Migration generates genetic diversity Interacts with and can overwhelm selection Metapopulations can explore genetic alternatives more efficiently than single large populations
What will happen to most new mutations?
Most new mutations will go extinct due to drift
gene flow
Movement of alleles into or out of a population due to the migration of individuals to or from the population
If the mutation rate increases, does the population evolve more slowly or more quickly? Why?
Mutation is of central importance in biology. It creates genetic variation, the raw material of evolution by natural selection, It can improve traits and organisms, but can also lead to phenomena like cancerous cells and antibiotic resistant pathogens. Increasing the mutation rate can accelerate evolutionary adaptation
What is the creative force in evolution?
Mutation: Without mutations, one genotype would get fixed in the population and then nothing could change
Refer to the graph showing fitness effects of mutations in the yeast, Saccharomyces cerevisiae. Which inference is not supported by the data shown in the graph?
Mutations yielding new stop codons have little effect on fitness.
Creationists criticize the idea of natural selection as a circular argument, or tautology, claiming "The fittest are those that survive, and survival is how fitness is defined." Why is our definition of natural selection not tautological?
Natural selection is measured by contribution to the next generation, not simply survival of an individual organism.
What are the conditions required for natural selection?
Natural selection needs variation among individuals, differences in fitness/reproductive success and variation that passes onto the next generation.
Lamarck's Model
New groups originate independently over time and then progressively increase in complexity
Does the figure below give sufficient evidence to show evolution by natural selection has occurred?
No. The figure doesn't support heritability of variation in beak height.
Which of the following is the best example of the evolution of an adaptation? a. Non-random survival and reproduction favors finches with broader beaks,increasing the bill size in the next generation. b. A predator eats snails with a striped shell at a higher rate than other snails.By chance the pink snails in the population have a low rate of striping. In the next generation, more pink-shelled snails are present. c. A population of sticklebacks in a lake have low levels of armor.Migrants from the ocean introduce genes for increased armor to the population. d. All of the above are examples of adaptive evolution.
Non-random survival and reproduction favors finches with broader beaks,increasing the bill size in the next generation.
What is plasticity?
Phenotypic plasticity can be defined as 'the ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions are not heritable.
What are examples causes of genetic drift?
Population bottlenecks Founder effects Who gets lucky enough to mate Who gets lucky enough to survive (particularly in small populations)
This is an important figure in the textbook... it shows the germline mutations for the coding regions in the genome. What would you expect the somatic mutation graph to look like?
Problem is, most of the mutations occur in the non coding genome (introns). The coding region only accounts for 1-2 % of the genome. Many more nonsynonymous mutations.
In the general principles in documenting the patterns of evolution, there are proximal and ultimate causes. What are they? Example: a male bird singing. Name the proximal and ultimate causes for this action.
Proximal causes are the immediate/mechanical biological phenomena. Ultimate causes are the historical causes, like natural selection. ex: A male bird singing proximal: action of hormones, structure & action of singing apparatus & brain operations ultimate: paste ancestors whose genes inclined singing may have been more successful in finding a mate.
Some cancers are evolving by genetic drift
See the slope, it indicates drift.
phylogenetic tree uses
Serve as models for reasoning about evolutionary history Predict and explain patterns of traits across taxa Infer origins of epidemics Quantify trends in biodiversity
Which term is defined as any consistent difference in fitness among phenotypically different classes of biological entities as a consequence of competition for mates?
Sexual selection
Imagine an absurdly small population of only 3 E. coli bacteria, one of which is resistant to antibiotics. However, there is no antibiotic in their environment. If, by chance, in the next generation, one of the sensitive E. coli dies and the resistant one divides, how much has the resistant allele frequency changed in that generation?
Since there is 3 in the population, 1/3 is resistant, which is .333% or 33% in first generation.
Where do somatic cells start on this fitness landscape?
Somatic cells start at the lower peak b/c they are designed to work within an organism
What are potential costs of dispersal?
Takes energy to move Exposure to predators Land in worse environment Less food More polluted More predators Fewer mates
Phylogeny
The evolutionary history of a species or group of related species
What Was The Last Eukaryotic Common Ancestor Like?
The last common ancestor would be a unicellular organism that is a hybrid between prokaryote + eukaryote
gene swamping
The loss of a locally advantageous allele cause by the influx of other alleles from other populations. Gene flow overwhelms local adaptation (s<<m; when migration is stronger than selection)
effective population size
The number of individuals that would give an idealized population (hermaphroditic population of constant size with no natural selection) the same strength of random drift as the actual population of interest
What is the difference between an ecological niche and a realized niche?
The particular range of conditions that species can tolerate, and how their physiological responses impact their geographic distributions, are commonly described in terms of their ecological niche The realized niche is typically smaller and describes the fraction of the fundamental niche that is actually occupied by a species.
genetic hitchhiking
The process by which a neutral or even disadvantageous allele is able to "ride along" with a nearby favorable allele to which it is physically linked, and thus increase in frequency.
Provide an adaptive and a nonadaptive hypothesis for the evolutionary loss of useless organs, such as eyes in many cave-dwelling animals. How might these hypotheses be tested?
There may be a metabolic cost to building a useless organ, and so individuals that have lost that organ would have a selective advantage. Alternatively, if an organ is useless, mutations that disrupt the development of that organ would be evolutionarily neutral and could spread to fixation by genetic drift. Competition experiments between variants that have retained versus lost the useless organ could reveal if those that have lost it have a selective advantage.
After graduation, you and 19 of your closest friends (lets say 10 males and 10 females) charter a plane to go on a round-the-world tour. Unfortunately, you all crash land (safely) on a deserted island. No one finds you and you start a new population totally isolated from the rest of the world. Two of your friends carry (i.e. are heterozygous for) the recessive cystic fibrosis allele. Assuming that the frequency of this allele does not change as the population grows, what will be the incidence of cystic fibrosis on your island?
Total pop of 20, 2 friends carry (heterozygous) ; make punnett square. Incidence = aa, cystic fybrosis is presenting .25 (.25)= .0625
How should the distribution of selective coefficients of somatic mutations differ from germline mutations?
We do not know the distribution of selection co-efficients of somatic mutations.
Consider a species of sparrow that originally lived only in Alaska but recently expanded its range through North America, then Central America, and finally South America. How would you expect heterozygosity for most loci to differ among populations in North America, Central America, and South America? Why? Which of those three regions would you expect to have the most genetically similar populations, and which the most different?
We expect to see a pattern similar to that found in human populations: highest heterozygosity in the oldest part of the species' range (North America) and lowest heterozygosity in the most recently colonized part (South America). This pattern would result because populations farthest from the original range have experienced the greatest number of bottlenecks. We also expect to see isolation-by-distance: populations in North and South America will be more different than either is from populations in Central America.
A species that has a high rate of long-distance dispersal is more likely to colonize new habitat. But that species may also be less likely to adapt to local conditions, because migration will be stronger than local selection pressures for many loci. In light of those considerations, when do you expect that increasing dispersal might result in the evolution of a larger geographic range, and when might it not?
When there are opportunities for long-distance dispersal to establish isolated populations, increased dispersal is likely to lead to larger geographic ranges. This is because a new isolated population that is established by long-distance dispersal is sometimes largely or completely free of later gene flow. (Consider the seeds of a continental species of plant that wash up on the shore of a remote oceanic island. There is a very good chance that no seeds of that species from the continent will ever wash up on the same shore again.) However, if new populations continue to receive immigrants from a source population, local adaptation can be prevented by gene swamping, and further expansion of the species' range prevented.
Would you expect sexual selection to increase or decrease adaptation of a population to its environment? Do the pleiotropic effects and good genes mechanism for the evolution of female preferences differ in their implications for adaptation to the environment?
Whether sexual selection increases or decreases adaptation of a population to its environment depends on the form of sexual selection. In the case of male conflict, some of the characters that aid males in defending territories and securing mates, such as size and weapons, could also be useful for avoiding predators and hunting. In the case of female choice, the good genes hypothesis inherently assumes that females pick males who are well-adapted to their environments so they can pass those adapted genes onto their offspring. Runaway selection can cause morphological extremes in color and size that make males more visible to predators and can be a physical burden. Sexual selection by sensory bias probably contributes little to environmental adaptation.
Which mutation is most likely to become fixed? a. A neutral or nearly neutral mutation in an extremely large population b. A beneficial mutation in an extremely large population c. A neutral or nearly neutral mutation in an extremely small population d. A beneficial mutation in an extremely small population
a beneficial mutation in an extremely large population
insertion
a common mutation when a segment of DNA is added to a chromosome. Some cause genetic disease, others play important roles in adaptation
missense mutation
a nucleotide-pair substitution that results in a codon that codes for a different amino acid
selective sweep
a process in which one allele increases in a population due to positive selection
duplication
a second copy is inserted + the process can be repeated- giving rise to a gene family with several copies at the original locus. Can lead to divergence and evolution of new biological functions
Pleitropy
a single mutation affecting multiple traits -virtually all mutations that have phenotypic effects show pleiotropy. -effects are often on seemingly unrelated traits -plays a key role in evolution : genetic alterations that alter one aspect have side effects on other aspects
population bottleneck
a type of genetic drift in which population size is sharply reduced due to some catastrophic event. In this case genetic drift increases
What are the relative fitness relationships for 3 possible genotypes if a beneficial allele (a) is over-dominant?
aa<Aa>AA
What are the relative fitness relationships for 3 possible genotypes if a beneficial allele (a) is dominant?
aa=Aa>AA
What are the relative fitness relationships for 3 possible genotypes if a beneficial allele (a) is recessive?
aa>Aa=AA
What are the relative fitness relationships for 3 possible genotypes if a beneficial allele (a) is partially dominant?
aa>Aa>AA
structural mutations
affect more than 1 DNA base (a few to a billion) Happens as errors when chromosomes are replicated. types: deletion, insertion, duplication, inversion, reciprocal translocation, fusions/fissions, whole genome duplication
regulatory mutation
affect regions such a promoters, introns and regions coding for the 5' UTR and 3' UTR segment of RNA 3 types: promoter, splicing and cryptic splice sites
What would cause a difference between the census (actual count) population size and the effective population size?
age, reproduction fitness, mutations, unequal proportion of M/F and restriction of genetic diversity
Evolution is the change in...
allele frequencies in a population over time
promoter mutation
alter consensus sequence nucleotides of promoters and interfere w/ efficient transcription initiation.
Define Organismal Fitness: How is it estimated?
an individuals ability to survive and reproduce estimated by counting offspring over time
intercalating agents
are chemical mutagens that slide between the stacked nitrogenous bases of the DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs. The result is during DNA replication, DNA polymerase may either skip replicating several nucleotides (deletion) or insert extra nucleotides (insertion)
nucleoside analogs
are chemicals structurally similar to normal nucleotide bases and can be incorporated into DNA during replication. They induce mutations b/c they often have different base pairings
poladenylation mutations
caused by a base pair substitution of the 5' AAUAAA 3' polyadenylation signal sequence and can block proper 3' processing of mRNA.
What is non-adaptive evolution?
change in allele frequency that does not result in a population becoming better adapted to its environment. Anything other than positive selection
background selection
changes in allele frequency due to selection on a linked locus
deletion
common mutation when a segment of chromosome is left out during replication. Most are harmful
The two major themes of On the Origin of Species are:
descent with modification and a variational theory of change.
Mating fiddler crabs use several types of sexual selection. Males battle each other for territory using their greatly enlarged claws. The territories preferred by females are those in the most physiologically stressful area, and only healthy males can maintain them for long. The males also raise their claws to signal females; those that reach the greatest heights are most noticeable because females are attuned to look upwards for predators. Which model of sexual selection is least likely to impact this mating system? a. Good genes mechanism b. Direct benefits c. Male-male competition d. All of the above
direct benefits
What does endemic mean?
endemic is a species restricted to a particular geographic region.
whole genome duplication
extreme type of mutation where meiosis produces a gamete that carries the entire diploid genome (rather than the haploid w/ one pair chromosome each). The result is offspring with 4 copies of each chromosome (tetraploidy). Since new species cannot interbreed with parental pop, a new species is born in one mutation.
T/F: Only reproduction advantages - not survival advantages - can drive selective sweeps.
false
How does fitness depend on environmental context?
fitness depends on the environment in which the organism lives. The fittest genotype during an ice age, for example, is probably not the fittest genotype once the ice age is over.
migration variance
for spatially continuous populations use migration variance
disruptive selection
form of natural selection in which a single curve splits into two; occurs when individuals at the upper and lower ends of a distribution curve have higher fitness than individuals near the middle
stabilizing selection
form of natural selection in which individuals near the center of a distribution curve have higher fitness than individuals at either end of the curve
Why is cancer an evolutionary disease?
fuel: variation (mutations in cells cause variation) engine: variation effects reproduction & survival (some mutate faster) traction: variation among cells is heritable (cells copy when they divide)
point mutation
gene mutation in which a single base pair in DNA has been changed
What is NOT an example of a secondary sexual trait? a. Long tails on widowbirds b. Gonads c. Antlers d. All of the above are examples of secondary sexual traits
gonads
Taxon
group or level of organization into which organisms are classified
Which of these conditions must be met in order for selection to act on a population? a. Heritable variation b. Differential reproductive success c. Consistent allele frequencies d. A population of 100 or more individuals
heritable variation and differential reproductive success
Increased migration (m) =
increased m = increased time genetic differences between them are erased
What are two types of frame shift mutations?
insertion and deletion (addition of a base; removal of a base)
How does geography affect species distribution?
insurmountable physical barriers: such as mountains, oceans, rivers, deserts, and, more recently, expansive human development. periodic physical barriers: such as in areas characterized by frequent flooding, fires, or volcanic eruptions. physiological barriers: temperature, soil and water chemistry, and precipitation present to dispersal. Because of these barriers, species distribute themselves and become isolated, forming new species unique to their ecological niche.
what is an evolutionary trade off?
is when a choice must be made between multiple things that are either incompatible or an increase in one thing might lead to a decrease in another.
What is LUCA?
last universal common ancestor; common ancestral cell from which all cells descended about 4 GYA (billion years ago)
Gene flow is quantified by
migration rate (m); the fraction of migrants arriving to a population. ex: if 120 individuals in a population of 1000 are immigrants 120/1000= .12
molecular clock
model that uses comparisons of DNA sequences to estimate phylogeny and rate of evolutionary change
Which forces of evolution typically increase the genetic diversity of a population?
mutation + migration
Which forces of evolution typically increase the genetic diversity of a population? (you may choose multiple answers)
mutation and migration
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide
Is then the evolutionary transition to multicellularity a difficult one or not?
not at all, since multicellularity has arisen more than twenty times in evolution"
Fissions
one chromosome splits to form two (responsible for the change in the # of chromosomes in a genome)
If an allele (e.g. antibiotic resistance) is at frequency p in a population, and there is no fitness differences between alleles (e.g., there is no antibiotic in the environment), what is the probability that that allele will go to fixation?
p the gamete pool of p's and q's; p's are at 30% of allele frequecy
The whole population is split into p's and q's, so p + q =?
p + q = 1
Hardy-Weinberg equation
p^2 + 2pq + q^2 = 1
Types of dispersal
passive: (pollen, seeds, spiders coral) active: swarms of grasshoppers, locust
what is positive selection?
positive selection is alleles beneficial to the species
common descent
principle that all living things have a common ancestor Species share some traits in common because they split from the same lineage
Hardy-Weinberg Principle
principle that allele frequencies in a population will remain constant unless one or more factors cause the frequencies to change
cryptic splice sites
produce new splice sites that replace or compete with authentic splice sites during pre-RNA processing
All fertility mutations..
reduce the fertility of the organisms
Imagine a new mutation, with no selective advantage (s=0), appears in a diploid population of 500. What is the chance that that mutant allele will drift to fixation?
s=0, selective co-e of 0 = neutral (no selection) diploid population of 500 = 500(2)= 1000 alleles 1/1000 = 0.001 chance it will drift to fixation
You observe a very narrow cline in the middle of a broadly distributed species' range. From this you could conclude that ____________.
selection is strong and migration variance is low
Some conservationists believe that increasing gene flow in isolated populations or species with limited individuals is a beneficial and necessary alternative to inbreeding depression and potential extinction. What are the concerns with genetic swamping? (choose all the apply)
small populations may be especially vulnerable to genetic swamping from large immigrant populations negative effects on the locally adapted variations creating hybrids
In promiscuous mammals, males often have greatly enlarged testicles compared to closely related monogamous species. What model of sexual selection best explains this observation?
sperm competition
Inversion
structural mutation that occur when a chromosome breaks in two places and the middle segment is re-inserted in the reverse orientation. Common feature in the evolution of a species. ex: the genomes of humans and chimps differ in about 1,500 inversions that become fixed in one lineage or another since our last common ancestor 7 million years ago.
Migration rate
tells us how quickly gene flow erodes genetic differences between populations. changeP = m (pm-p) pm= allele freq in migrants p= freq in focal pop b4 migration
What tends to happen to new mutations that are: Neutral
tends to go extinct quickly
What is trait fitness?
the average fitness of organisms with a particular trait
reciprocal translocation
the exchange of chromosome segments between 2 homologous chromosomes ex. translocation heterozygotes can have reduced fertility which leads to genetic isolation
Fst =
the proportion of the total population genetic variance due to differences between subpopulations = how different are the subpopulations
A monophyletic group (also called a clade) is defined as:
the set of species derived from one common ancestor.
What is Evolutionary Biology?
the study of the origin, maintenance, and diversity of life
True or false: The number of migrants per generation necessary to homogenize two populations does not depend on the population size.
true
Fusions
two chromosomes join to form one(responsible for the change in the # of chromosomes in a genome)
genetic drift
unbaised, random genetic drift is stronger in small populations, causes genetic variation to be lost, causes identical populations to become different, can fix alleles without the benefit of natural selection
What is a derived character?
A new character that evolved on a lineage.
Using this tree, which statement is accurate?
A seal is equally related to a horse and a whale
What happens to the allele frequencies over time in a population that is in HardyWeinberg equilibrium?
Allele frequencies will equal out, or stay roughly constant over time (which means no evolution)
What are the necessary and sufficient conditions for natural selection?
Differences in reproduction and/or survival Variation in the population Heritability of the relevant traits
directional selection
Form of natural selection in which the entire curve moves; occurs when individuals at one end of a distribution curve have higher fitness than individuals in the middle or at the other end of the curve
lineage
Group claiming a common ancestor
Given this graph of allele frequencies over time in a population, what could you infer about how the population size changed around generation 300?
Red went into a bottleneck
Which is more important, reproduction or survival?
Reproduction
In general, synonymous polymorphisms tend to be more common than nonsynonymous polymorphisms. Why might that be?
Synonymous polymorphisms do not change the amino acid and so are less likely to be acted on by natural selection. In contrast, nonsynonymous polymorphisms are often deleterious and thus removed rapidly by natural selection.
What can we not test with the tree of life?
The causes of chance events like individual mutations Events that have no historical trace left today
What is a selective coefficient?
The relative difference in fitness caused by a mutation
What happens to most new beneficial alleles when the enter the population, regardless of whether they are dominant, recessive or over-dominant?
They tend to go extinct due to drift
What are the two types of photoproducts?
Thimer-dimer and 6-4 photoproduct
T/F: When an allele is common in a normal-sized population, even a small advantage (s >> 1/Ne) will tend to drive it to fixation.
True
What is pleiotropy?
When a single mutation effects multiple traits
