Evolution Exam 1

Distinguish between the terms "natural selection" and "evolution"

Evolution- an outcome Natural Selection- a process

Summarize the molecular clock hypothesis. How does it apply to phylogenetics?

Many mutations change an individual's DNA, but not its phenotype (most are not exposed to natural selection)

What are "maternal effects"? How might they affect estimates of heritability? Provide an example.

Maternal effects- The environmental effects that are due to nutrient stores or hormonal contents of eggs ex/ a pregnant woman exposed to famine during gestation

What are "point mutations"? What causes them to occur?

Point mutation- a single base substitution in the hemoglobin gene Caused by: 1) random errors in DNA synthesis 2) random errors in the repair of sites damaged by chemical mutagens or high-energy radiation

Define polyploidy. Why is it common in plants but rare in animals?

Polyploidy- a way of self-fertilization - common in plants and rare in animals because self-fertilization is more common in plants and rare in animals

The blue-footed booby has 3 alternative phenotypes for male plumage color- red, orange, or gold. Determine the fitness values for each phenotype assuming the average number of offspring the R, O, G birds have are 5, 3, and 1.5 respectively

R- 5/5= 1 O- 3/5= 6 G- 1.5/5= 0.3 The frequency of red birds would increase in the next generation

Distinguish between "relative" and "absolute" dating of rocks. Include in your answer an explanation of the term "half-life"

Relative dating- Determining the order of past events without necessarily determining their absolute age Absolute dating- The use of radioactive decay to age rocks and therefore the fossils within them Half-life- The amount of time for one half the original amount to be transformed

What is retrotransposition? What is its significance to evolutionary biology?

Retrotransposition- when a processed mRNA is reverse transcribed by reverse transcriptase - if it becomes integrated into one of the main chromosomes, then the genome has acquired a duplicated copy of the original gene

What are reversals? Provide an example.

Reversals- changes in the DNA sequence data ex/ changing the 5th position back to the ancestral state later in the evolution of a group

Why might excessive use of antibiotic and other antimicrobial agents be a public health concern? How is this growing concern related to evolution of natural selection?

The treatment of the patient is more difficult and the antibiotic-resistant bacteria may spread to other people

Explain how research on the mummichog serves as evidence of selection to match climatic conditions

There is an enzyme which acts as a better catalyst at lower temperatures than an enzyme from the south

Were Boag and the Grants able to establish any kind of molecular (genetic) basis for the variation they observed in beak morphology? Explain.

There was a BMP4 (bone morphometric protein 4) It signaled molecules that helps sculpt the shape of bird beaks

Describe how the fields of comparative anatomy and embryology served Darwin well as evidence of change through time

They helped to see that there were fundamental similarities under the obvious physical differences among species

Briefly describe Mathers and Harrison's experiment with fruit flies. What was the purpose of the study? What did they conclude from their work?

They wanted to see how flexible traits were to selection (the number of abdominal bristles) They selected offspring with the highest and lowest number of bristles and found that there were 20 generations of selection over the course of a year

"Homology is the guiding principle behind most biomedical research". What does this mean? Back up this statement with at least one example in support of your explanation

This is the reason why medical researchers can obtain valid results when testing the safety of new drugs in mice or studying the molecular basis of a disease in rats ex/ Monkeys and apes are often the preferred experimental subjects because aspects of their behavior and brain structures are homologous with those of humans

Explain what is meant by the statement "the genetic code is universal"

This means that all living things share a common evolutionary heritage

What is CCR5? What is its function? What is its significance to human health?

- CCR5 is a human gene - codes for cell surface protein on WBC's and used as a co-receptor by most sexually transmitted strains of HIV-1

Summarize/describe how Peter and Rosemary Grant's research on G. fortis test and validate all of Darwin's postulates.

- Focused on the medium ground finch - There was a strong correspondence between relatives regarding genes (beak depth) - Ground finch species with larger beaks make BMP4 mRNA earlier and in a larger quantity than species with smaller beaks - Only large birds with deep narrow beaks can crack and eat Tribulus fruits successfully

Summarize the "modern synthesis" version of Darwin's postulates.

- Individuals in populations vary based on the mutation of creating new alleles - Individuals pass their alleles on to their offspring - Some individuals are more successful at surviving and reproducing than others - Individuals that survive and reproduce are those with alleles and allelic combinations (these best adapt to their environment)

Briefly summarize the potential fates of duplicated genes. Might there be adaptive value in such mutations? Explain.

- when a DNA sequence is duplicated, the original gene should continue to produce a normal product - gene duplication results in new possibilities for gene function ex/ globin gene family- genes that make up globin family are thought to be a product of gene duplication events

Explain the connections between inversion and genetic linkage. Why do inversions so often lead to gene linkage?

- when inversions are heterozygous, the inverted sequences can't align properly when the homologous synapse spring Prophase I of meiosis - alleles inside inversion lock and are inherited together as a single supergene

Briefly describe the 4 biological characteristics discussed in class that ALL organisms share in common.

1) Composed of one or more cells 2) Carry out metabolism 3) Synthesize and use ATP for energy 4) Encode hereditary info in DNA

Both mutation and meiosis create genetic variation in populations. Distinguish between the kinds of variation the 2 processes are capable of creating.

1) Crossing over- leads to new groupings of alleles on individual chromosomes 2) Independent assortment- leads to new mixtures of chromosomes in the resulting daughter cells

The "traditional view" of classification of organisms assumed the greater the time since 2 species shared a common ancestor, the more different they should be. However, similarity is NOT necessarily a good predictor of how long it has been since 2 species shared a common ancestor. Explain the 3 primary reasons for why this is the case.

1) Evolution can occur very rapidly at some times and very slowly at others 2) Evolution is not unidirectional (sometimes species evolve in one direction and then back the other way 3) 2+ species independently evolve similar traits

Summarize the 3 fundamental reasons why chromosome-level mutations are important in evolution.

1) Inversions may lock groups of alleles into tightly liked "supergenes" 2) Polyploidization may lead to the formation of new species 3) Genome duplication provides massive amounts of redundant gene sequences that may then diversify

State and briefly describe the 2 types of chromosome-level mutations that are particularly important in evolution.

1) Inversions- result from a multistep process that starts when radiation causes 2 double strand breaks in a single chromosome 2) Genome duplication- when cells have double the number of chromosomes of the parent cell

State and describe the 4 key issues that complicate how heritability is estimated in bird species such as G. fortis.

1) Misidentified paternity- a chick's social father is not always the biological one 2) Conspecific nest parasitism- even the social mother may not be the biological parent 3) Shared environments- any correlation that is due to relatives sharing their environment inflates the estimate of heritability 4) Maternal effects- environmental effects that are due to nutrient stores or hormonal contents of eggs

List and briefly describe the 4 key types of mutation that have significant evolutionary impact on populations. Additionally, summarize their mechanisms and evolutionary significance.

1) Point mutation- creates new alleles, chance errors during DNA synthesis or during repair of damaged DNA 2) Chromosome inversion- alleles in the inversion will be transmitted together as a unit, breaks in DNA are caused by radiation or other insults 3) Gene duplication- redundant new genes may acquire a new function by mutation, unequal crossing over during meiosis or retrotransposition 4) Genome duplication- may create new species (massive gene duplication), errors in meiosis or (in plants) mitosis

List and briefly describe the two most common processes that result in gene duplication.

1) Retrotansposition- when a processed mRNA is reverse transcribed by reverse transcriptase to form a double stranded DNA segment 2) Unequal cross-over- a chance mistake caused by the proteins involved in managing the genetic recombination that occurs during meiosis

Summarize the set of assertions (claims about the pattern of life's History) key to the Theory of special creation

1) Species don't change through time 2) Were created independently of one another 3) Were created recently

State and briefly describe the 3 primary components of evolutionary fitness discussed in class. Include in your answer an example illustrating each component.

1) Surviving- the ability to avoid predators ex/ A hare outrunning a fox 2) Mating success- a living thing attracts the most mates based on a trait ex/ Upstream guppies attracting mates with their coloration 3) Fecundity- The number of offspring per mating ex/ How much offspring a female produces from mate to mate

Summarize the three key observations about the fossil record that helped provide Darwin with solid evidence of change through time

1) The fact of extinction- When Darwin had written "The Origin", extinct plants and animals were being found in rock layers that had been found in many times and places 2) The Law of Succession- a correspondence between fossil and living forms from the same locale 3) Transitional forms- species are descended with modification from earlier forms and that fossils represent past populations

State and describe Darwin's 3 conditions ("postulates") necessary for evolution by natural selection to occur within a population

1) Variation- Individuals with some traits are favored over individuals with alternative traits 2) Heritability- The sexed differences must have a genetic basis 3) Differential survival and reproduction- Some individuals are more successful than others at surviving and producing offspring just because of their phenotype or behavior

Summarize the 3 theorized ways natural selection may act to maintain significant genetic diversity within a population.

1) rare individuals 2) heterozygotes 3) different alleles at different times and places

Describe how the drought of '77 on Isla Daphne Major proved to be a pivotal turning point in the Grants' research, providing evidence of evolution by NS in the G. fortis population.

84% of G.fortis disappeared and most died of starvation - Decline in seed availability - Only a fraction of the population survived to reproduce - During future draughts ('80 and '82), 19% and 25% of G. fortis died

What is a phylogenetic tree?

A graphical summary of the evolutionary history (describes pattern and timing of events that occurred when species diversified)

Explain how the genetic code itself serves as evidence for evolution

All organisms studied to date use the same codons to specify the same amino acids to be incorporated into proteins

Define altruism. Does it occur in nature? Why or why not? Provide an example in support of your argument.

Altruism- the practice of selfless concern for the well-being of others - It does occur in nature because most of the time, living things protect others around them ex/ Vampire bats sharing their food

Summarize the central dogma of molecular biology.

An explanation of genetic information within a biological system

What are inversions? Describe how they happen. What are the evolutionary implications of inverted segments of DNA?

An inversion is comprised of a double strand break in a chromosome - caused from radiation - after breakage, a chromosome segment can detach, flip, and reanneal in its original location

Distinguish between homologous and analogous structures. Provide examples of each.

Analogous structures- body parts derived from different ancestral structures ex/ wings of birds and butterflies Homologous structures- structures derived from the same body part in a common ancestor ex/ pectoral flippers on a whale and front legs on a horse are derived from the same bones in an ancestral vertebrate

Distinguish between artificial and natural selection and provide an example of each

Artificial selection- breeder selects for the desired traits ex/ Dog breeds (all members of the same species because they can all interbreed and produce fertile offspring) Natural selection- environmental conditions determine which individuals produce more offspring ex/ Birds preferring taste of red bugs over green bugs and as a result there will be more green bugs and fewer red bugs

Explain how molecular homology is central to many of the advances of genetic engineering

By placing human genes into bacteria, this could result in genetic flaws being shared among humans or other animals if the bacteria spreads

What is character "polarization"? What is an outgroup comparison? Explain the how systematists use character polarization and an outgroup comparison to construct a cladogram.

Character polarization- a determination of whether some character states are either ancestral or derived Outgroup comparison- method used to assign character polarity - Systematists use character polarization to determine if the character states are either ancestral or derived from something

What is a "clade"? Provide an example.

Clade- a group of organisms believed to have evolved from a common ancestor ex/ The metazoa

Describe the relationship between beak size in G. fortis and seasonal rainfall on Daphne Major.

El nino ('83) resulted in an abundance of small, soft seeds which resulted in a strong selection for smaller birds with shallow beaks - Smaller birds favored in wet years while large birds favored in draught conditions

What is a "preadaptation"? Provide an example.

When a trait used in an original way eventually gets elaborated by natural selection into a new structure

Explain how genome duplication can lead to sympatric speciation.

When diploid and tetraploid populations are genetically isolated and on their way to becoming separate species

Describe what is meant by the phrase "Ontogeny recapitulates phylogeny". How does it provide evidence for evolution?

When embryos of different types of vertebrates often are similar early on, but become more different as they develop This is evidence or evolution because the embryos change as they develop

Does it matter which of the 3 nucleotides in a given codon experiences a point mutation? Why or why not? Explain.

Yes it does matter because the amino acid will be affected (subsequent protein)

Explain how bacterial resistance to antibiotics serves as an example of evolution by natural selection

Your body acts as the environment and an antibiotic is prescribed to you in order to kill the bacteria

What are vestigial genes? Provide an example

ex/ CMAH enzyme gene- helps synthesize a sugar used as a cell surface marker

The amount of genetic variation in most populations is extremely high. Why is so much allelic diversity present in most pops? Summarize the 2 modern views (theories) put forth by the evolutionary biologists to explain this diversity.

- There are dozens or even hundreds of different alleles present in most genes within most populations 1) The balance or "selections theory"- genetic diversity is maintained by natural selection 2) The neutral theory- most of the alleles at most polymorphic loci are functionally and selectively equivalent and are maintained by genetic drift

Population variation in the value of a given trait (e.g. beak depth in G. fortis) is a product of differences in genes and environments. Using G. fortis as an example, describe how a researcher might circumvent the issue of environmental effects on phenotype when estimating heritability.

- You could collect young chicks from natural nests and move them to the nests of randomly chosen foster parents - When the chicks grow up, calculate the mid offspring and mid parent values for both biological and foster parents

Summarized the observed relationship between the degree of environmental stability and mutation rates. Provide an example from class.

- a few mutations may have little or no detectable effect on fitness

Summarize Baer et al's ('05) work with roundworms. Why might this study be considered both groundbreaking and controversial?

- created experimental families from 2 different populations of each of 3 roundworm species - each population and each species has a different mutation rate - organisms may share a common mutation rate

How might biologists recognize past genome duplication events in extent species?

- descendant species might retain only a portion of the originally duplicated genes (the portions that have acquired new functions)

Contrast the classical and modern views of genetic variation. Explain the term "wild type" with respect to the classical view of genetic variation?

- determine the genotypes of a large sample of individuals in a population - usually looking directly at the DNA of the alleles themselves

Describe the experiments (both of them) conducted by Dee Denver and colleagues studying C. elegans. What conclusions did they draw? What was the significance of her findings?

- established many independent families - each family maintained in most benign environmental conditions possible to minimize impact of natural selection - found total of 30 mutations (each worm carried about 2.1 new mutations in its nuclear genome) - Also studied mutation rate in mitochondrial DNA - mutation rate estimated to be an order of magnitude higher than the rate observed for nuclear DNA

What is it about genome duplication that has led biologists to suggest there might be a correlation between genome duplication events and bursts of evolution during the history of life?

- gene duplication provides massive amounts of redundant gene sequences - it doubles the amount of genetic material present

If mutation rate is a trait that varies among individuals within populations, then when are lower or higher mutation rates advantageous? Provide an experimental example from class in support of you answer

- higher mutation rates may be adaptive when organisms colonize new environments to which they are poorly adapted ex/ Arjan de Visser et al ('99)- compared how fitness changed over time in E. coli populations with normal and high mutation rates - when bacteria-free mice were injected with equal numbers of E. coli, the mutator cells initially had a larger fitness advantage

Summarize the process of unequal crossing over. What role does it play in evolution?

- homologous chromosomes don't synapse correctly during Prophase I of meiosis - results in one chromosome that contains a deletion and one that contains a redundant stretch of DNA

Do populations of different species actually have distinct mutation rates? Summarize/describe experimental evidence that supports your answer.

- mutations in polymerase increased error rate and overall mutation rate - mutants that increased accuracy were slower than more error-prone mutants - point mutation rates depend on how efficiently mistakes in DNA synthesis are corrected

Explain how CCR5 and its alternative allele ∆32 effect susceptibility to HIV? How common is the ∆32 allele? Describe how this question can be addressed within a population.

- one CCR5 gene has a 32-base pair deletion in the gene sequence - individuals who are homozygous for the allele with the deletion lack CCR5 on the surface of their T cells (don't get infected with HIV) - a result of this would be that HIV-1 visions can't bind to the cells to initiate an infection

Describe how alternative alleles for DNA polymerase serve as evidence for population and/or individual variation in mutation rates in the bacteriophage T4.

- some mutations decreased the rate at which polymerase made errors during DNA replication and reduced overall mutation rate while other mutations increased this

How do biologists measure the overall amount of genetic variation present in natural populations? More specifically, how do they measure the diversity of alleles present at a particular gene? Provide an example to illustrate your explanation.

- the one best allele is considered to be the "wild type" while others are considered mutants and expected to be rare ex/ Harris ('66) and Lewontin and Hubby ('66)- found that instead of containing one wild type at a very high frequency, most populations harbor an array of alleles

Using mice as an example, explain how selection can favor gene duplications in specific gene families.

- there were 1,296 paralogous genes involved in olfactory reception - duplicated genes are common and the size of gene families varies greatly

What causes polyploidy to occur in the first place?

It occurs where individuals contain both male and female gonads and can self-fertilize

Summarize the Law of succession. Explain how it serves as evidence of change through time

Compared a fossil and living form from the same place This evidence for change through time because it showed that today's species displayed a strong resemblance to their recent ancestors

Describe complimentary base pairing. What are DNA polymerases? What are their functions? How might DNA polymerase activity lead to novel mutations?

Complimentary base pairing- provides a mechanism for copying hereditary material (one strand serves as the template for making a copy of the other) DNA polymerase- responsible for copying DNA in cells If the DNA polymerase inserts the wrong base, this would result in a mismatched pair that must be repaired (if the repair is made, a mutation is made)

Distinguish between Darwin's natural selection and Lamarck's inheritance of acquired characteristics. Provide an example that illustrates these "ideas". How might Lamarck's ideas be tied in with "cultural evolution"?

Darwin- proposed natural selection as the mechanism of evolution Lamarack- Individuals passed on to their offspring boy and behavior changes acquired during their lives ex/ ancestral giraffes with short necks had stretched them to reach leaves (this neck extension was passed on to future generations leading to long necks) This might be tied to cultural evolution based on the fact that the neck extension would just be a part of a new generation

NS is not forward looking. What does this mean?

Each generation is descended from the survivors of selection by the environmental conditions that prevailed in the generation before - Offspring may not be adapted to new conditions if environment changes

What are fitness tradeoffs? How might they influence selection on a given trait? Provide an example from class.

Fitness tradeoffs- When traits that increase fitness in one area decrease fitness in another area ex/ Guppies with greater coloration to attract mates are more likely to be predated upon

Describe the neutral theory of genetic diversity.

Genetic diversity is maintained because it is not eliminated by natural selection

Summarize the principle of uniformitarianism. What role did it play in the formulation of Darwin's Theory of Evolution?

Geological processes taking place now operated similarly in the past Helped to realize that earth was unimaginably old

Define heritability. Describe how Peter Boag measured heritability in G. fortis beak depth on Daphne Major.

Heritability- Proportion of variation observed in a population that is due to variation in genes Peter Boag measured heritability through beak depth (was genetically based and can be passed to offspring)

What causes genome duplication?

Homologous chromosomes may fail to segregate during meiosis I or if sister chromatids don't separate properly during meiosis II

What are homologous structures? Analogous structures? Provide examples for both

Homologous structures- Structures with different appearances and functions that are all derived from the same body part in a common ancestor Analogous structures- Structures that have non homologous similarities

Distinguish between homoplasy and homology?

Homoplasy- when a trait has been gained or lost independently in separate clades over the course of evolution Homology- the similarity of traits can be explained by common ancestry

Distinguish between micro and macroevolution

Microevolution- Can be directly observed by monitoring natural populations Macroevolution- Can find evidence of this by examining the bodies of living organisms

Distinguish between monophyletic and paraphyletic groups.

Monophyletic groups- clades or lineages, contain derived characters that were shared Paraphyletic groups- include some, but not all descendants of a common ancestor

Define genes, alleles, and mutations.

Mutations- any type of change in the base sequence of DNA Alleles- versions of the same gene that differ in the base sequence Genes- stretches of DNA that code fora distinctive type of RNA (protein product)

Explain the statement "NS acts on individuals, but its consequences occur in populations"

Natural selection may affect a certain living thing, but the population is affected by the consequences ex/ smaller birds dying due to there being more draught conditions resulting in the a larger population of larger birds

Briefly put forth an argument for why NS does not/cannot lead to "perfection". Provide at least one example in support of your argument.

Natural selection will not necessarily be in the organism's favor all the time ex/ The male mosquito fish's anal fin is modified to serve as a copulatory organ - Females tend to prefer larger gonopodia, but this creates a drag (slow escape)

Describe how the stickleback of Loberg Lake serve as an example of microevolution

Observing the bony plates in marine and freshwaters stickles directly

Explain why only a small fraction of the species that ever existed are known from fossils (be as specific as possible)

Only a few species such as whales and earlier forms of birds were being discovered

What are paralogs? Provide an example. Distinguish paralogs from orthologs. How might orthologous genes be used in the construction of a cladoram?

Paralogs- genes that are duplicated and then diverge in sequence ex/ members of alpha and beta globin clusters in humans

What is molecular homology? Provide an example of molecular homology discussed in class

Shared flaws in organisms suggest common ancestry ex/ CMT1A repeats- genetic flaw that both chimps and bonobos share

Describe the molecular basis of sickle cell anemia (be specific). Who discovered it?

Sickle cell anemia is caused by a change from glutamic acid to valine at a single position in the protein (a protein defect) - discovered by Vernon Ingram

Summarize the principle of parsimony. How is it used evolutionary biologists?

Simpler explanations are preferred over more complex explanations - when its applied, the preferred tree is the one that minimizes the total amount of evolutionary change that has occured

Define and provide an example of a "vestigial structure". How do they serve as evidence for evolution?

Structures that don't have any apparent function, but resemble structures their ancestors had ex/ Boa constrictors have hip bones and rudimentary hind legs By resembling structures from their ancestors, this would be evidence for evolution

What are "supergenes"? Describe how D. subobscura provides evidence of natural selection on supergenes (be specific!). Additionally, explain the "geographic cline" in inversion frequency observed in D. subobscura populations in the Americas.

Supergene- a group of alleles that are locked in an inversion and locked together - geographic cline looks at change in frequency of an allele or inversion - populations had expanded along each coast and developed the same clines in inversion frequencies found in the old world - correlated with same general changes in climate type

What are synapomorphies? Provide an example illustrating their utility in cladistics.

Synapomorphies- arise in ancestral populations and are passed on to descendants

Distinguish between synonymous and nonsynonymous substitutions. Which of the two typically has the most significant effect (if any) on phenotypes?

Synonymous substitutions- point mutations that result in no change Nonsynonymous substitutions- point mutations that result in an amino acid change (this one would have the most significant effect on phenotypes)

How might altruistic behaviors increase the altruist's fitness?

The beneficiaries of the behavior are close relatives or reciprocate

What is Archaeopteryx? What is its significance to evolutionary biology?

The most famous transitional form, first known bird found in Bavaria in 1862 It is a direct decent from dinosaurs which indicates that today's birds are feathered dinosaurs

Traditionally, mutation rates were estimated by studying large populations of organisms and counting the number of offspring with observable mutant phenotypes in each generation. What's wrong with this method?

The mutant phenotypes were knock out or loss-of-function mutations (these changes in DNA inactivate a gene)

The polymerase responsible for copying viral genes in a study conducted by Furio et al. ('05) exhibits "a fundamental trade-off between accuracy & speed". Explain the meaning/significance of this statement with respect to mutation rates.

The mutants that did increase accuracy were much slower than those that were error prone

What is fecundity? How does it affect an individual's fitness?

The number of offspring per female ex/ large female frogs and fish lay more eggs than smaller females and result in leaving more offspring to the next generation

What is evolutionary "fitness"? How would we determine the most "fit" phenotype?

The number of surviving offspring left in the next generation We can determine the most fit by looking specifically at the one that produces the greatest number of offspring