Exam 1 Evolutionary Biology

Give one argument against evolution posed by scientific creationism. Provide evidence against this argument.

"Because the earth is 6000-8000 years old there is not enough time for Darwinian evolution to occur" - Radiometric dating shows that the earth is very old "Because organisms progress from simpler to more complex forms evolution violates the second law of thermodynamics" - The second law, entropy, only applies to closed systems - The earth is an open system with the sun supplying energy to the system - Organisms do not necessarily evolve to be more complex

Explain what HAART is and why it is more effective for HIV+ patients than a single drug therapy.

(Highly Active Anti-Retroviral Therapy) = more than two drugs. HAART is highly effective, with life expectancies for HIV+ patients within a few years of the HIVpopulation. Even patients with AIDS have vastly lengthened lifespans. It‟s much harder for resistance to evolve to multiple drugs at once.

Which of the following is NOT an example of homologous structures:

- Bat wing and bird wing**** - Human arm and bat wing - Horse leg and mole leg - Dolphin flipper and human arm

"Natural selection is not perfect."

- Can only work with the variation present in each generation - - Natural selection could not make the perfect beak because the genes for it were not present (in finches).

Darwin's Four Postulates

- Individual species are variable - Some variation is heritable (passed to offspring) - More young are born than can survive - Survival and reproduction are not random

Which of the following is a FALSE statement about the Maximum Likelihood method?

- Maximum Likelihood assumes a particular probabilistic model of sequence evolution and then calculates for each tree the probability of the data given the tree. P(data|tree) - It uses all available data, even autapomorphies, in determining the tree - It is utilized by assuming a particular probabilistic model of sequence evolution and then calculating P(tree|data) for each tree**** - These are among the most accurate methods to reconstruct phylogenies - The choice of probabilistic model is based on the data

Explain the statement "Mutation is random"

- Not all conceivable mutations are equally likely to occur - Not all loci or regions within a locus are equally mutable - Environmental factors may influence the RATE of mutation (UV radiation, carcinogens, etc...)

Homologous structures can be (select all that apply):

- Structural: organs or skeletal elements of animals and organisms that, by virtue of their similarity, suggest their connection to a common ancestor. - Developmental: Anatomical similarity due to derivation from a common embryological source - Genetic: a gene inherited in two species by a common ancestor. While homologous genes can be similar in sequence, similar sequences are not necessarily homologous.

What aspects of our lives does evolution move directly influence?

- Survival - Reproduction

Name and describe the two fields of systematics. Briefly compare AND contrast the fields.

- Taxonomy • Classifying organisms in groups - Phylogenetics • Reconstructing evolutionary relationships

Explain how HIV's development of AZT resistance satisfies Darwin's postulates.

- There is variation among virions in their resistance to AZT - The ability to distinguish between AZT and thymidine is inherited - Not all virions are able to infect T cells and reproduce - The virions that distinguish AZT the best produce more offspring and are naturally selected for

What does it mean for a point mutation to be neutral? To be beneficial? To be deleterious?

- Usually neutral - Sometimes beneficial • Lactase persistence in humans • Antibiotic-resistance in bacteria (for the bacteria!) • ccr5-Δ32 - Sometimes deleterious • Albinism • Color blindness • Hemophilia in terms of the ability of an organism to survive and reproduce*

A scientific theory...

- does not rely on unsupported speculation. - is based on using reasoning and evidence to explain a wide variety of observations - can be revised as new hypotheses are tested and new data is collected.

When HIV replicates, it must use a host of enzymes and pieces of machinery. Name and briefly describe 3 such things necessary for HIV replication

- the viral protease (PR), that converts the immature virion into a mature virus through the cleavage of precursor polypeptides - reverse transcriptase (RT), responsible for the conversion of the single-stranded genomic RNA into double-stranded proviral DNA - the integrase (IN) that inserts the proviral DNA into the host cell genome

In a sample of cows, there are 10BB, 2Bb, and 8bb genotypes. What is the frequency of the B allele?

0.50 0.55*** 0.45 0.40 10/20 + 1/2 (2/20) = 0.55

List and briefly explain the four assumptions regarding characters for phylogenetic analysis

1. Homology 2. Character states have genetic basis 3. Characters are independent 4. Character evolution reflects organismal phylogeny

After infection, when is the viral load of HIV RNA the lowest?

A few weeks after the onset.

Define analogy (homoplasy) and give an example of an analogous structure

A homoplasy is a character shared by a set of species but not present in their common ancestor. - evolution of the eye which has originated independently in many different species. When this happens it is sometimes called a convergence.

Uniformitarianism

A principle that geologic processes that occurred in the past can be explained by current geologic processes Earth much more than a few thousand years old

Theory is often used in everyday language - i.e. "I have a theory about how to solve this problem." Describe how a scientific theory is different from an everyday theory. Give an example of a scientific theory

A scientific theory does not mean unsupported speculation - a mature, interconnected body of statements, based on reasoning and evidence, that explains a wide variety of observations Examples: Germ Theory of disease, Theory of relativity, theory of gravity, atomic theory.

Which of the following is FALSE about transitional forms?

A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. -There are species with living transitional forms - Transitional forms are usually direct ancestors of living species **** - Large-scale evolutionary changes are often accounted for in extinct transitional fossils between two living target species - Phylogenies generated based on transitional forms can be updated as new transitional forms are discovered

Explain what conditions would lead to HIV evolving less virulence in a society

Access to ART reduces viral load, which reduces transmission rates dramatically (to nearly zero with full compliance). In places with low incidence and high ART compliance, it‟s hard for HIV to spread

Briefly describe an adaptation, a preadaptation, and the relationship between the two.

Adaptation: a trait that increases an individual's fitness in its environment (enhanced by natural selection) Preadaptation: an adaptation which serves a different purpose from the one for which it evolved.

Which of the following is TRUE about natural selection in AZT-resistant strains of HIV?

An individual's population of HIV virions can evolve resistance to AZT if AZT medication alone is taken over a long period of time

True or false: Autapomorphies are informative when generating phylogenetic trees.

Autapomorphy: Some traits are derived along a single lineage - Not useful for estimating relatedness An autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon.

Which of the following lists the steps of the HIV life cycle in the correct order?

Binding à DNA Splicing à Translation à Budding

Briefly explain the concept of bootstrapping and how it is used in determine phylogenies.

Bootstrapping statistically evaluates confidence in nodes • Repeated sampling to see if tree differs from chance Shows confidence in a tree - Bootstrap values are percentages of the number of times the same branch arose after repeated sampling - Bootstrap support over 70% indicates that the correct relationship was probably found - Investigators usually report any bootstrap value over 50%

Describe one way that natural selection can produce new traits while acting on existing traits.

Can select from variation present • E.g., cannot instantly create a new beak for cracking a certain fruit - Over time, natural selection can produce new traits - New mutations every generation for natural selection to act upon

Explain what it means for cladograms to display a bifurcating pattern of cladogenesis.

Cladistics refers to a biological classification system that involves the categorization of organisms based on shared traits Three principles of cladistics: 1. Any group of organisms is related by descent from a common ancestor 2. There is a bifurcating pattern of cladogenesis 3. Change in characteristics occurs in lineages over time There is a bifurcating or branching pattern of cladogenesis, when a lineage splits, it divides into exactly two groups

Explain the differences between a cladogram and a phylogram

Cladogram: A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed Phylogram: A phylogenetic tree is an evolutionary tree that shows the evolutionary relationships between different groups of animals. What does a phylogram need that a cladogram does not? Why? Informative branch lengths

What form of evolution causes analogous structures? What causes this form of evolution?

Convergent evolution creates analogous structures or 'homoplasies', those which have similar forms or functions between diverged species, but were not present in the common ancestor of the two Occurs when two species from unrelated lines develop the same traits or features. This happens because they live in similar habitats, and have to develop solutions to the same kind of problems

Describe one of the problems that Darwin's ideas faced based on prior knowledge during his time (hint: there are 3). Describe how the belief was challenged, the evidence to support or rebuff it, and what we now know

Darwin did not know how variability was created - Thought that variation in organisms would be used up eventually - We now know new variation is created continuously by mutation Darwin did not know how traits were inherited - Believed in blending inheritance • Individual traits would be lost by merging with other traits - After Mendel was re-discovered we know that alleles are inherited independently Lord Kelvin established that the earth was 15-20 million years old based on Earth‟s rate of cooling - Not enough time for all species on earth to evolve - Did not account for convection or radioactive decay, incorporation of both proved that Earth was much older, sufficiently old for all species to evolve

Briefly describe the process of radiometric dating. What information can be gained from this process?

Different isotopes have appropriate half-lives for dating different time scales you can measure the amount of original and daughter isotopes in a rock sample and calculate the age of the rock

Explain the statement "Natural selection is backward looking."

Each generation is a product of selection by the environmental conditions from the generation before

True or false: There is only one cause of natural selection. Justify your answer.

False

True or false: All point mutations cause changes in proteins. Explain your answer.

False.

True or false: All DNA mutations within exons cause changes in an amino acid sequence. Explain your answer.

False. DNA mutations within coding regions (= exons) are either synonymous or nonsynomomous: - Synonomous = silent • Does not change amino acid sequence - Nonsynonomous = nonsilent • Changes amino acid sequence

True or false: When HIV virions are exposed to AZT, the individual virions change in order to survive in the presence of AZT and this leads to AZT resistance. Explain your answer.

False. When HIV virions are exposed to AZT or finches are exposed to changes in seed availability, those selected individuals are not changed - They just live through selection event and produce more offspring than others - The populations of finches or virions then change, not the individuals

True or false: All postulates must be independently verified. Support your answer.

False. A postulate is a statement that is assumed true without proof. Some postulates cannot be proven.

True or false: It is always a bad thing for scientists to be wrong. Explain your answer in 3 sentences or less

False. It is a good thing for scientists to be wrong, new technologies and evidence cause us to refine and change our hypotheses regularly. Our understanding of the world continually improves.

True or false: All synapomorphies are symplesiomorphies but not all symplesiomorphies are synapomorphies. Explain your answer.

False. It's the opposite. The main difference between synapomorphy and symplesiomorphy is that in synapomorphy, two or more taxa share a character with their recent common ancestor while, in symplesiomorphy, the character shared by the two or more taxa occurs in their earliest common ancestor.

True or false: Classifying organisms is easy and once an organism is given a classification, this can never change. Justify your answer

False. Today our challenge is correcting taxonomy such that we only group together organisms that are related due to shared evolutionary history, regardless of outward similarity. This does change and is debated on heavily (example: turtle wars).

Explain transitional forms

Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants Dinosaur > Dinosaur that looks like a bird > Bird

Steps of the Scientific Method

Four steps: 1. Description of a phenomenon or group of phenomena (usually but not always based on observation). 2. Formulation of a hypothesis to explain the phenomena. 3. Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations (hypothesis must be testable). 4. Performance of experimental tests of the predictions by several independent experimenters and different kinds of properly performed experiments.

List and describe three chromosomal alterations that introduce new genes to a population

Gene duplications - Result from unequal crossing over - Extra copy is free to accumulate mutations • Subject to weaker natural selection (duplicate) Overprinting in Tymoviruses - Cause mosaic diseases in plants - Tiny genome of THREE genes - Two genes overlap and are transcribed in different reading frames - Phylogeny shows that overprinting occurred in evolution of tymovirus family Retroposition - Processed mRNA is inserted into genome - Chondrodysplasia in dogs Chromosomal alterations: Inversions; - Can disrupt linkage • Phenomenon where genes near each other are inherited in groups - Cannot align properly with homologs • Results in dysfunctional gametes Polyploidy - Entire extra sets of chromosomes - Tetraploid, octoploid, hexaploid, triploid, etc. - Common in plants and rare in animals

Which of the following is NOT a source of variation?

Genetics Genotype-by-Environment Interactions Use-and-disuse*** Environment

Which of the following are the correct taxonomic levels in bionomical nomenclature?

Genus species

What is HIV, how does it spread, and how does it cause AIDS?

HIV (human immunodeficiency virus) is a virus that attacks cells that help the body fight infection, making a person more vulnerable to other infections and diseases. It is spread by contact with certain bodily fluids of a person with HIV, most commonly during unprotected sex (sex without a condom or HIV medicine to prevent or treat HIV), or through sharing injection drug equipment. AIDS is the late stage of HIV infection that occurs when the body's immune system is badly damaged because of the virus.

Which of the following answers (2) are the correct pairing between HIV subtype and source?

HIV-1 from chimpanzees HIV-2 from sooty mangabeys

Which of the following enzymes do HIV therapies NOT target?

Helicase

Briefly explain the concept of heterozygosity. How does this compare to the percent of polymorphic loci in a population?

Heterozygosity—the condition of having two different alleles at a locus—is fundamental to the study of genetic variation in populations. As the average frequency of heterozygotes across loci -As the fraction of loci that are heterozygous in the genotype of the avg. individual

Define homology and give an example of a homologous structure

Homology: similarity resulting from common ancestry homologous structures: mammalian forelimbs

Explain why it is useful to use a variety of reconstruction methods in constructing phylogenetic trees. What does it mean for methods to give congruent results?

If different methods give congruent answers we typically have more confidence in the phylogeny

The cells of which system are targeted by the HIV virus?

Immune System

Individuals in a species evolve to conditions...

In their past In their present In their future Individuals do not evolve****

Which of the following causes loss-of-function mutations?

Insertions Point mutations Transposable genetic elements Deletions

"Natural selection is dynamic."

It isn't set in stone, and changes given the environment and may reverse/continue.

Which of the following is the correct order, from highest to lowest, of taxonomic levels within the hierarchical system of classification?

Kingdom > Phylum > Class > Order > Family > Genus > Species

Lamarck's Theory of Inheritance of Acquired Characteristics.

Lamarck hypothesized that species evolve through use and disuse and the inheritance of acquired traits (long necks on giraffes) or epigenetics as a whole.

Compare and contrast Maximum Likelihood Method and Bayesian Methods

Maximum Likelihood Method: assumes a particular probabilistic model of sequence evolution and then calculates for each tree the probability of the data given the tree. P(data|tree) - Calculates the Likelihood statistic, which helps estimate the topology of the tree - Uses all data, even autapomorphies and invariant sites - Uses a particular model of evolution to help estimate the topology (tree shape) and branch lengths of the tree Bayesian Method: Similar to likelihood methods except P(tree|data) not P(data|tree) • Ask what the probability is of a particular tree being correct, given the data and a model of evolution. • Bayesian approaches are typically coupled with Monte Carlo (MC) approaches to search, tree-space‟

Define Maximum Parsimony method. What assumption is this method is based on?

Maximum Parsimony method minimizes total amount of evolutionary change in a tree Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves

Describe an advantage and a disadvantage to morphological characters. Describe an advantage and a disadvantage to molecular characters

Morphological character advantages: well established characters, less expensive, can examine fossil taxa, can look at more individuals more often. Morphological character disadvantages: genetic basis often poorly understood. molecular character advantages: huge number of characters, closer to real genetic basis, better models of how characters evolve, more amenable to certain analyses (Maximum likelihood & Bayesian analysis). Molecular Character Disadvantages: more expensive, and cannot examine fossil taxa.

Which of the following was NOT discovered by Darwin?

Natural selection Theory of evolution*** Sexual selection Descent with modificatio

Imagine that all genetic mutations in a species of porcupine suddenly ceased. Which of the following do you expect to see?

No new alleles No new genes No evolution

Define the term "outgroup" and explain why it is useful to use the outgroup method in creating phylogenetic trees.

Outgroup = a closely related taxon that is used instead of the ancestor Outgroup represents the likely ancestral state of the character in the ingroup An outgroup is used in phylogenetic analyses to figure out where the root of the tree should be placed (and sometimes which character state is ancestral on the tree).

Genotype can be determined by examining which of the following?

Phenotype Proteins DNA sequences

evidence that refute the claim that the Earth is young.

Plate tectonics says no. Radiometric dating says no. Magnetic field striping says no. Fossil record says no.

Which of the following is NOT an example of a molecular character that can be used to reconstruct a phylogeny?

RFLPs Allozymes Fossils *** DNA sequences

Explain how HIV becoming resistant to AZT therapy is an example of natural selection

Random mutation acted upon by natural selection enables HIV, the virus that causes AIDS, to rapidly neutralize the effectiveness of drugs designed to combat it. This is natural selection acting on HIV for lowmistake reverse transcriptase, conferring a newly evolved trait AZT resistance. This is viral microevolution that happened within each person on AZT therapy, and AZT as a longterm stand-alone treatment for HIV failed

Describe what it means for a trait to "skip a generation.

Recessive traits like red hair can skip generations because they can hide out in a carrier behind a dominant trait. The recessive trait needs another carrier and a bit of luck to be seen. This means that it can sometimes take a few generations to finally make its presence known

True or false: There is redundancy in the genetic code. Explain your answer

Redundancy of genetic code - Not all point mutations cause changes in proteins - 4*4*4 = 64 codons, but only 20 amino acids

Explain how mutations may accumulate following a gene duplication event

Result from unequal crossing over - Extra copy is free to accumulate mutations • Subject to weaker natural selection (duplicate)

Briefly compare and contrast the two theories explaining the persistence of genetic diversity.

Selectionist theory - Natural selection favors allelic diversity Neutral theory - Polymorphic alleles are functionally equivalent so they are not selected against

Synapomorphy

Shared derived characters common to all members of a group

Which of the following is NOT a proposition of special creation?

Species were created independently Earth is young Lineages split and diverge **** Species are immutable

Which of the following is NOT a problem faced in taxonomy?

There is no one "true" classification. It is governed by formal international rules*** There must be human opinion involved. New data may necessitate changes to classifications.

Which of the following is TRUE about theories?

They can only be proven They can only be disproven *** They can be both proven and disproven New evidence that disobeys a long-standing theory can be discarded for simplicity

A point mutation results in a change from G to C (G to C). Which of the follow statements are true? There may be one or more than one correct answer.

This is a transversion. This is a change between purine and pyrimidine.

True or false: Convergent evolution produces homoplasies, a.k.a. homologous structures.

True. Convergent evolution produces homoplasies a.k.a. analogous structures , convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. Example: Desert dwelling ant specialists from two different families !

Define a vestigial structure and give an example

Vestigial structures = rudimentary or functionless - Snakes and whales with hind legs - Human goosebumps, tail bone, appendix - Pseudogenes

True or false: We are able to predict the likelihood and type of mutation that will occur in an organism and when it will occur. Explain your answer.

We can only predict the probability (likelihood) of a mutation occurring, but not which mutation will occur, or when. The chance that a particular mutation will occur is not influenced by whether or not the organism is in an environment in which that mutation would be advantageous. - Natural selection does not see, think, plan or feel, it just acts on whatever variation exists

True or false: Non-phylogenetic approaches are almost always superior or equal to phylogenetically-informed approaches. Explain your answer.

We should always question the methods used to reconstruct the phylogeny to be confident in the results Phylogenetically-informed approaches are almost always equal or superior to non-phylogenetic.

Briefly explain two reasons why mutation rates are variable.

Why are mutation rates variable? - DNA polymerase varies in error rate - Mismatch repair systems vary in effectiveness - Some species have higher or lower mutation rates overall • Viruses: high mutation rate • E.coli: low mutation rate - Coding regions have fewer mutations than noncoding regions • Natural selection (specifically, purifying selection)

If a specifies does not exhibit phenotypic plasticity, what do you expect to see in the species? What do you expect to see on the reaction norm graph?

With no phenotypic plasticity or genotype-byenvironment interaction the phenotype is the same in different environments Reaction norm = phenotypic expression of a single genotype across a range of environments The steepness of the slope of a reaction norm graph indicates amount of plasticity of that genotype... very flat if plasticity is not shown.

Explain why mutations are so important. What would happen if mutations did not occur?

Without mutation, no new alleles, new genes, and no evolution

Are human populations evolving as a result of the HIV pandemic?

Yes. Some individuals are repeatedly exposed to HIV without becoming infected. Others become infected but are Long-Term Nonprogressors, maintaining CD4 > 500 without ART

"survival of the fittest"

a bad way to describe natural selection. Survival of the fittest = survival of the survivors

Compare and contrast paraphyly and polyphyly. Which is more common? Are either of them problematic? If so, which and explain your answer.

a group is paraphyletic if it consists of the group's last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. A polyphyletic group is a set of organisms, or other evolving elements, that have been grouped together but do not share an immediate common ancestor. Polyphyly is less common and more worrisome

Briefly describe a ring species and give an example of this concept.

a ring species is a connected series of neighboring populations. While each can breed with those nearby, in the end at least two populations are no longer able to interbreed as both time and their environment has left them too distantly related, even though they are technically the same species. a situation in which two populations which do not interbreed are living in the same region and connected by a geographic ring of populations that can interbreed. Example: salamanders reached the southernmost part of California, the separation had caused the two groups to evolve enough differences that they had become reproductively isolated.

Natural selection increases

complexity adaptations*** simplicity size

Law of Succession.

extinct species in the fossil record were succeeded in the same region by similar species extinct species are ancestors of living species

Natural selection is...

fixed random dynamic*** irreversible

Most parsimonious tress minimize ___________ to give best estimate of phylogeny

homoplasy (a character shared by a set of species but not present in their common ancestor)

Natural selection acts on ____ but evolution occurs in _____.

individuals; populations

It is difficult to treat HIV because...

is a virus that expands and multiplies using the bodies immune system. The immune system works to tackle the virus, but the more it does this, the more HIV is able to replicate. Over time - usually many years - without treatment, the virus always comes out on top. The second challenge for HIV drugs and vaccines is that the virus has a very high turnover - billions of copies every day in a person who is not on treatment - and makes small errors or mutations which can lead to the easy development of drug resistance

The origin of higher species and taxa (__________) can be explained in terms of natural selection acting on individuals and changing populations (__________).

macroevolution; microevolution

What type of group consists of a common ancestor and ALL organisms that descended from this ancestor?

monophyletic

Phylogenetic trees are constructed when systematists use ______________.

more than one character

Explain the Transmission Rate Hypothesis.

natural selection favors high rates of virulence for STIs when partner exchange is frequent, low rates of virulence when partner exchange is infrequent - A society shifts from monogamy to promiscuity: increase in virulence - A society shifts from promiscuity to monogamy. What do you expect to happen to HIV virulence over time in this society? decrease in virulence with safer sex practices.

Another term for unresolved node is ________.

polytomy (an internal node of a cladogram that has more than two immediate descendents)

Describe domestication and give an example of this concept.

process by which plants and animals are genetically modified over time by humans for traits that are more advantageous or desirable for humans. - dogs!

Mutation is a ____ process

random

What is heritability? Why is it important? Why is it difficult to measure?

statistic used in the fields of breeding and genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population. Heritability is the single most important consideration in determining appropriate animal evaluation methods, selection methods and mating systems. • Parent-offspring correlations are influenced by: - Misidentified paternity (= "extra-pair mating") - In birds, nest parasitism - Maternal effects - Shared environments

_____________ define evolutionary branching points on a phylogenetic tree.

synapomorphies

Darwinian fitness

the ability of an individual to survive and reproduce in its environment

phenotypic plasticity

the ability of an organism to change its phenotype in response to changes in the environment. Freshwater snails (Physa virgata), provide an example of when phenotypic plasticity can be either adaptive or maladaptive. In the presence of a predator, bluegill sunfish, these snails make their shell shape more rotund and reduce growth.