Evol FINAL

Which character pattern will unambiguously resolve four taxa.

0101

After it was challenged by other species concepts, the phrase "actually or potentially interbreeding" was added to the original definition of the Biological Species Concept to attempt to:

Accommodate populations that might be different species in allopatry.

Whereas the textbook gives one standard definition of a monophyletic group (an HCA and all of its descendants, Dr. Theriot offers another, called the "scissors test". The latter test differs from the former in that the scissors test does not require any statement about ____:

Anything not already in evidence.

Latent variation occurs in traits that are controlled by many loci. We learned that this occurs:

Because extreme combinations of alleles at multiple loci are increasingly unlikely with an increasing number of loci.

The Phylogenetic Species Concept is Dr. Theriot's favorite concept in part because it is applicable to species in allopatry and to asexual species because it identifies species operationally and conceptually as:

Independent evolutionary lineages whether sexual or asexual. Is applicable to species in allopatry.

What fundamental evolutionary trade-off summarizes the Disposable Soma Hypothesis:

Rapid growth in somatic cells is selected for at the expense of fidelity of reproduction.

The Antagonistic-Pleiotropic Hypothesis leads to accumulation of deleterious mutations through:

Selection.

What results are expected in terms of genetic diversity when it comes to the founder and bottleneck effect?

genetic diversity is reduced

Inbreeding increases the number of _____________ in a population.

homozygotes

Effective population size was estimated for a population of Padre Island Blue-Phased Gophers as much lower than the observed or censused population size. This means it is likely that:

that the reduction in heterozygosity at neutral alleles from generation to generation is higher than expected.

Extinction is a concept best associated with:

the idea that variation exists and is "sorted out" by natural phenomena.

The number of possible gamete types produced by sexual recombination is at least 2^n, where n is:

the number of chromosome pairs

k/2N, where k is the number of copies of an allele, and N is the number of organisms, represents:

the probability of fixation by drift.

We can measure distances among loci along a chromosome by observing:

the rate at which linkage disequilibrium breaks down linkage disequilibrium among these loci.

Under mutation-selection balance, even if an allele has a selective advantage, it will never go to fixation. Why?

there will be increases in one allele (3 pts), but that it never goes to fixation because it "back mutates" to the deleterious or less beneficial allele (4 pts).

Stalk height in a population of wild okra plants is determined by two alleles at a locus, T and t, which display incomplete dominance. TT individuals are tall, Tt are medium height, and tt are short. There are 36 short plants out of 100. How many plants do you expect to be tall if the population is in HW equilibrium?

16

Define "homoplasy" in terms of character pattern on a tree, and give an example of what sort of evolutionary event it might represent.

A homoplasy is a character incongruent with any monophyletic group (alternatively: incongruent with the larger body of evidence, with all other characters). It might represent convergence (alternatively, horizontal gene transfer, reversal. There may be others).

In lecture we learned that a taxon is:

A named monophyletic group.

A population bottleneck leads to

Accelerated rates of genetic drift which return to lower rates after the bottleneck.

A simplified view of the Atavistic Hypothesis suggests that a general explanation of many adult cancers is at least partly a result of:

Ancient mechanisms in cells inherited from our single celled ancestors to reproduce at high rates.

Somatic Hypermutation is an important component of our immune system's ability to mach the evolution that occurs in pathogens. This process is triggered or occurs:

As a consequence of contact of a mature B-lymphocyte antibody with an antigen.

Which of the following ideas provides a problem for Darwinian thought?

Blending inheritance is the primary method of transmission.

Somatic Recombination in the vertebrate immune system is analogous to Variable Glycoprotein Switching in trypanosomes in that:

Both generate a great deal of variability through some form of chromosomal rearrangement of existing intragenomic (within the genome) variability.

The fact that phylogenetic trees exhibit fractal patterns is consistent with the fact that OTUs can be:

Both individual organisms and are ideally monophyletic groups of species

Referencing Tree Set Alpha --Which cladogram(s) is (are) different from Cladogram A?

C

RNA viruses have higher mutation rates than DNA viruses. This is in part due to the fact that

Deamination of cytosine to uracil is not detected in RNA viruses.

Statement: Allopatric models of speciation follow Occam's Razor with regards to the need to invoke evolutionary processes, meaning that once populations are separate, only a single simple process like drift or positive selection are necessary to drive differentiation (phenetic concept), evolution of novel characters (phylogenetic concept), or permanent breeding barriers. Sympatric or parapatric models (which don't physically separate populations) require more assumptions, usually needing to invoke:

Disruptive selection and assortative mating.

The heavy chain immunoglobulin locus has Variable, Diversity, Joining and Constant domains. The light chain locus lacks the ________________ domain. Together the heavy and light chain glycoproteins produced form about 1011 variants in a process called___________.

Diversity; Somatic Recombination.

The speciation models that require that populations be physically separated are:

Dumbbell and peripheral isolation.

If the unfortunate Simon Wagstaff had taken BIO 370, he would have learned that one strategy to lengthen human life spans might be to delay reproduction as long as possible. This might work because it would:

Essentially transform many late-acting mutations into early-acting mutations.

The slope of the regression line calculated from measures of the same trait in known parents and known offspring in the laboratory represents:

Explains covariance in the trait between the parent and offspring. Is h^2.

Evolutionary theory suggests that childhood lymphoma could actually be a result of selection related to:

High rates of mutation in B-lymphocytes.

What does it mean for two alleles to be "identical by descent"? Give an example in terms of a hereditary chart.

Identical by descent means that alleles are identical in two or more individuals because the alleles were inherited from a recent common ancestor. When close relatives mate, the offspring tend to carry alleles at many loci that are identical by descent.

A cladogram differs from a phylogram in that the latter:

Illustrates, through relative branch lengths, the amount of evolutionary changes over each branch.

Among mammals, only camelids lack light chain immunoglobulin proteins. The apparent loss of light chain immunoglobulin loci:

Is a synapomorphy for camelids. May reduce the initial diversity of their immunological response.

Senescence:

Is the inevitable by-product of other adaptations.

Purifying selection is indicated when:

Ka is less than Ks.

It is perhaps ironic that viruses may not be alive, yet they can be said to evolve. Selective forces that drive viral evolution are:

Largely the same as those that drive evolution in living creatures.

From an evolutionary perspective, that most cancers occur post-peak reproductive years may be attributable at least in part to the:

Mutation Accumulation Hypothesis. Disposable Soma Hypothesis.

The Hardy-Weinberg model assumes that none of the five evolutionary processes are at work. What are these five processes?

Natural selection Drift Nonrandom mating Mutation Migration

The molecular clock is an effective null hypothesis because it posits that:

Neutral substitutions occur at the same rate as neutral mutations regardless of population size.

What is Occam's Razor and how do we apply it to phylogenetic inference?

Occam's Razor is the proposition that, when faced with more than one explanation for an observation, we accept the one that requires the fewest assumptions. In phylogenetic analysis, we explain as much similarity as possible as due to descent with modification (alternatively, we accept the hypothesis that minimizes homoplasy.)

You want to follow the textbook's recommendation to utilize species concepts in combination to best understand speciation, but the species you are interested in are asexual. Thus you are restricted to combining:

Phenetic and Phylogenetic Species Concepts.

Referencing TREE DELTA - The sister group to Annelida is:

Pogonophora + Vestimentifera

Referencing TREE DELTA- Ignore letter labels. The numerical values at nodes are bootstrap support values. — We are systematists and have just calculated Tree Delta. Based on previous work, we had been considering naming the 5 groups as shown by the big names next to the brackets. However, we only want to put names on well supported monophyletic groups. We decide not to name ___________________________.

Protostomes because they lack bootstrap support lower than 50%.

Cold-blooded tetrapods are typically thought of as reptiles. They occupy the "middle" of the tree with birds and mammals occupying the "edges" of the tetrapod tree. E.g., in Tree Beta above, we might consider OTUs 1, 2, 3, 5, 6, 7 to be tetrapods, with 1 as mammals and 2 as birds, and 2,7,3,5,6 to be reptiles. Why then is it wrong to say that reptiles give rise to birds and to mammals?

Reptiles are not monophyletic and so they are not a natural group. Thus they never existed in nature and, having never existed, could never have given rise to something.

RNA viruses have higher mutation and evolutionary rates than DNA viruses, with retroviruses having the highest mutation rate of all, allowing for higher potential to adapt to a new host. As a consequence of this:

Retroviruses are among the most likely to jump from one host species to another. Effective treatment of retroviruses is improved by considering their ecological and evolutionary dynamics.

Recall that Dr. Theriot postulated that Stephanodiscus yellowstonensis was a derivative species and that S. niagarae was the progenitor species. What characteristics might we expect these two species to show with respect to one another?

S. yellowstonensis would have fewer mitochondrial types and less genetic diversity.

The Biological Species Concept main strength is:

That it defines species on the basis of a fundamental evolutionary process, sexual reproduction.

The Phenetic Species Concept main strength is:

That it is operationally repeatable and subject to statistical analysis.

Late-acting deleterious mutations are unlikely to be removed from populations for the same reason that late-acting beneficial mutations are unlikely to increase in populations. The ultimate, common reason is:

That most populations are well past their peak fecundity and have been reduced greatly in number, so that fitness effects are relatively small.

Two sister species each have several autapomorphies (both are good phylogenetic species.) Given this and no other information, we would expect, given only the following options, to find additional data that support:

That the species evolved allopatrically following the dumbbell model.

The Apolipoprotein 1 mutation provides modest survival benefits to an individual which has it (in areas with trypanosomes that cause sleeping sickness), even though it apparently contributes to a significant overall reduction in lifespan. Thus its frequency is higher than expected in parts of the world with this trypanosome. This is an example of:

The Antagonistic Pleiotropy Hypothesis.

Cells in tissues exposed to harsh environments (e.g., skin, digestive tract) have to replace themselves more rapidly than other tissues, causing them to perhaps invest more in cell reproduction than fidelity in DNA reproduction. Germ-line cells, however, are likely undergoing selection for fidelity of copying of DNA rather than speed of cell reproduction. The trade-offs involved are known as:

The Disposable Soma Hypothesis.

In the Midas - Arrow speciation example, the phylogenetic tree recovered Midas populations as non-monophyletic (resolved a series of branches more or less like rungs on a ladder, and Arrow was recovered as a single branch. Remember, too, that the Midas populations were geographically isolated from one another. Thus, the Midas populations collectively only rigorously fit:

The Phenetic Species Concept.

Consider a locus with two alleles, A and a. Under which of the following scenarios will the frequency of the A allele increase?

The fitness of AA and As individuals are higher than the fitness of aa individuals.

You have read the snake evolution story and heard about it in class. Why would we say that, if vestigial limbs occurred, we would find them in snakes and not in earthworms although both lack legs? You must put this in terms of what you would expect in terms of both initial assessment of homology, secondary assessment of synapomorphy of the larger group to which snakes belong, and in terms of Character Transformation Series.

The initial assessment is that leglessness is a synapomorphy (alternatively: homologous). Incongruence with other characters (alternatively: with the final tree or tree based on all evidence) suggests that leglessness is, in fact, homoplasic (alternative: convergent) rather than synapomorphic/homologous. Leglessness > legs > Lost legs is the Character Transformation Series

In a typical progenitor-derivative species pair, drift is most likely to affect:

The initial population of the derivative species.

Our ingroup is composed of all modern (living) species. They have the putative (proposed) synapomorphy of Character X (they are the only living creatures known to have Character X). We are looking for the best outgroup taxon for our analysis. They share Character Y with a living species. We are creating a data matrix of only "hard parts" of our species, which fossilize.

The living species with Y, but not X should be used as the outgroup.

Individuals homozygous for the CCR5 Delta 32 mutation have resistance against M-trophic HIV strains but are more susceptible to several forms of viral-caused encephalitis. Which statements below are true.

The missing amino acids prevent the HIV from recognizing and attacking the white blood cell, but then causes the cell to fail to interact with the virus as it normally would.

You are studying two populations of South Padre Island Red-nosed Blue-footed Gophers, one above Mansfield Pass and one below Mansfield Pass. You notice that the northern population has 16 microsatellite alleles and the southern population has 3. You conclude that:

The southern population may have recently been through a bottleneck. The southern population may have been recently derived from the northern population.

Congruence among phylogenetic trees calculated with independent datasets is a powerful tool because:

There are so many trees possible for even a few taxa, that the odds of obtaining the same tree are low.

To say that a group of OTUs share a hypothetical common ancestor shared by no other OTUs is the same as saying:

These OTUs are monophyletic.

How is the founder effect similar to the bottleneck effect in terms of population size?

They both involve relatively small population sizes, and are both dominated by drift

In the Arrow/Midas Cichlid sympatric speciation hypothesis, the investigators had to investigate not only the biology and genetics of the species in question, but had to understand the geological history of the larger geological basin in which they occurred. This is because:

They had to eliminate allopatric speciation and subsequent dispersal as a hypothesis.

Without mutation or migration, only positive or negative selection on combinations of loci maintain haplotypes in linkage disequilibrium indefinitely, whether or not loci are physically linked. True or false? Why?

This is a true statement because recombination will otherwise eventually eliminate linkage disequilibrium.

Not surprisingly, many mutations are lethal. However, many mutations are not lethal.

This is because many mutations are synonymous.

If the Apoyo Midas population were more closely related to some other Midas population than it was to the Apoyo Arrow population:

This would have been a problem for the hypothesis of sympatric speciation because it would mean that Midas in Apoyo Lake did not share an immediate common ancestor with the Apoyo Arrow species.

The smallest group of organisms that share a common evolutionary trajectory, is called the evolutionary species concept. Its main utility is:

To serve as a general model for other species concepts for which we may develop testable criteria.

If there 8 possible transversions and only 4 possible transitions, why do we observe more transitions than transversions?

Transversion mutations distort the helical axis backbones (2 pts), making them more likely to be detected and corrected by DNA repair mechanisms (2 pts).

Why is underdominance relatively rare in natural populations? Answer needs to be in terms of what kind of equilibrium and what happens to allele frequencies

Underdominance is an unstable equilibrium (4 pts). Therefore any perturbance away from a critical point (the point of equilibrium) will drive 1 allele to fixation or its frequency to 1 (or will drive 1 allele to be lost or frequency go to zero). (4 pts)

Which phenomena decrease Neffective relative to Nobserved and so are important to conservation and management of wildlife because they reduce heterozygosity and genetic diversity?

Uneven sex ratios. Selection pressure.

Which of the following might involve epistasis?

When selective consequence at one locus are affected by an allele at another.

Under what condition will likelihood be statistically inconsistent?

When the model is misspecified.

We want to test for whether our population is undergoing non-random mating. Which variable will interest us the most?

Whether observed heterozygosity is larger or smaller than expected heterozygosity based on observed allele frequencies.

What are the effects of natural selection, mutation, and migration on the amount of genetic variation within and between populations?

Within a population, mutation and migration increase variation and natural selection (except balancing selection) decreases variation. Between populations, mutation increases variation and migration decreases variation. Natural selection can either increase or decrease variation between populations, depending on the selective conditions.

We make an observation that about 60% of species with blotched color patterns lives in forests which have blotchy patterns of light and dark. We further note that about 65% of species with striped patterns live in grasslands which will have more vertical patterns of light and dark. In both cases, other species might be solid colored, striped, or have some other pattern. Why can we NOT conclude that each pattern is a camouflage adaptation to its environment?

Without a phylogeny, we cannot judge the independence of our data points.

You conduct a phylogenetic analysis of several closely related species which overlap in distribution, and find that for each pair of sister species, both have accumulated several autapomorphies.

You conclude that these species likely evolved according to the dumbbell allopatry model.

The point at which at which two branches on a phylogenetic tree meet is known as:

a node and a hypothetical common ancestor to all OTUs beyond that point

Neutral theory offers a null model against which to test the near-neutrality or neutrality of DNA sequence differences by comparing inferred nonsynonymous substitutions with synonymous substitutions. Synonymous substitutions provide:

an estimate of the rate of substitution expected for nonsynonymous sites under the notion that the allelic changes have no effect on fitness.

Extreme phenotypes in continuous traits can be revealed as latent variation. This is most likely to occur when the following two phenomena are combined:

extreme selection and/or assortative mating (like breeding with like).

Referencing Tree Beta -- OTU 4 is more closely related to:

it is equally related to both

Darwin's theory of evolution by natural selection was challenged by:

lack of knowledge about the nature of inheritance of traits. the lack of observation on intermediaries of complex traits.

An important characteristic of scientific hypotheses is that they:

make predictions about natural phenomena that can be tested and rejected

Select the words that best complete this sentence. A Wright-Fisher population is __________ likely to exhibit ________ in allele frequencies than a __________ population because the latter __________.

more, drift, Hardy-Weinberg, less subject to chance events.

In a haploid species, the primary source of genetic variation from generation to generation is:

mutation

What is the founder effect?

occurs when a few individuals from one population colonize previously unoccupied territory

Drift and selection can enhance or counteract each other depending on strength of selection and population size. When a population is large, compared to circumstances in a small population, weak (e.g., s=0.002) positive selection on a new mutation is initially:

overwhelmed by drift, but has a stronger net effect if and when the allele frequency increases to modest levels.

The proportion of homozygotes (A1A1) in a population at Hardy-Weinberg Equilibrium is 36%. What is the frequency of heterozygotes? Show your work.

p2 = 0.36 (1 pt) p = 0.6 (1 pt) q = 0.4 (1 pt) 2pq = 2 * 0.6 * 0.4 = 0.48 (3 pts)

A scientist in 1900 discovers traits in offspring (pink flowers) that are intermediate between both parents (one with red flowers, one with white). To test whether this is due to blending inheritance or codominance/incomplete dominance, the scientist crosses offspring with one another. Today we know that the cross would have been likely to produce offspring with:

red, white, and pink flowers.

Epistasis is best defined in evolutionary biology as

situations where selection eliminates some allelic/loci combinations and creates correlations among alleles among loci.

Which conditions will result in higher rates of loss of heterozygosity in neutral allele frequency?

small population size and assortative mating.

The experiment of Luria and Delbrűck is a demonstration of the stochastic nature of mutation, that is mutation is not directed towards creating more fit individuals. The key observation is that bacterial resistance to the phage was:

variable from replicate to replicate.

The concept or process that best accommodates biological diversification is:

variational processes.

Natural selection can act on:

viability and fecundity