Biol2040 Solved Study Aid (Post-Midterm Material) (W2021) PDF

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BIOLOGY 2040 EVOLUTIONSecond Half FINAL EXAM STUDY AIDHere is a collection of questions, topics and concepts from the second half of the course. It is intended as a study aid as you prepare for the final exam. The final exam is cumulative and will consist of approximately 85% from material after the...

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BIOLOGY 2040 EVOLUTION Second Half FINAL EXAM STUDY AID Here is a collection of questions, topics and concepts from the second half of the course. It is intended as a study aid as you prepare for the final exam. The final exam is cumulative and will consist of approximately 85% from material after the midterm and 15% from before the midterm. 1. What is the cost of sex and why does the cost exist? Disadvantages of sex: takes time, exposure to predators, need to find mate (if outcrossing), and ‘cost of sex’ (cost of males, cost of meiosis). The cost of sex is 2! It’s because the asexual-reproducing females reproduce twice as fast, and so the gene of asexual reproduction reproduces twice as fast as the sexual reproduction gene. The entire population of the asexualreproducing female will also be only females.

2. What is Muller’s ratchet? In what kinds of populations should it be most relevant? Muller's ratchet is a process in which absence of recombination, especially in an asexual population, results in accumulation of deleterious mutations (harmful mutations) in an irreversible manner (bottleneck situation). It only works in small populations (so it is NOT universal) and it lowers the fitness of species.

3. What is the Red Queen hypothesis for the maintenance of sex? The Red Queen hypothesis states that if the current genotypes are no longer favored, then sex (re)creates the favored types; that organisms have to evolve quickly because parasites are evolving quickly.

4. What is linkage disequilibrium. What generates it? What breaks it down? How calculate? Linkage disequilibrium is the nonrandom association of alleles at different loci, which can also be on different chromosomes.

It is created / generated by: - Selection of multilocus genotypes - Random genetic drift (and mutation) - Population admixture

It is destroyed by: - Genetic recombination (as sex brings disequilibrium (D) to 0) - Sex shuffles multilocus genotypes

5. Fisher’s runaway process of sexual selection Definition: In species whose reproductive success of one sex depends on winning the favor of the other (such as polygamous birds), sexual selection (by itself) will increase the intensity of the preference and the feature preferred, together at ever-increasing speed, which will cause great and rapid evolution of particular conspicuous characteristics until natural selection’s direct or indirect effects stop this process. How the process starts: - variation in male trait (display) and female preference - assortative mating and genetic correlation - natural selection favors extreme males (or RGD). Results: - Favors females with preferences for extremes: * Sons: higher trait value * Daughters: higher preference - Positive reinforcement (self-reinforcing) - Runaway evolution

6. Good genes hypothesis for female choice, and evidence for it Good genes hypothesis: an explanation which suggests that the traits females choose when selecting a mate are honest indicators of the male's ability to pass on genes that will increase the survival or reproductive success of her offspring.

Evidence: Grey tree frogs example - It was hypothesized that females prefer males with longer calls than males with shorter calls. In the experiment, 38 out of 53 times, the females bypassed a male with shorter calls to get a male with longer calls. - To test whether that males with longer calls have better survivability genes, they did a study where they took eggs from the same female and half of those eggs were fathered by long-calling male and the other half were fathered by shortcalling male. - The result was that the offspring fathered by the long-calling males had significantly higher fitness than their maternal half-siblings fathered by shortcalling males.

7. Phenotypic variance: definition and components Phenotypic variance is a measure of the dispersion of observed phenotypes around the expected (average) value. Components: It is calculated by the addition of genetic variance and environmental variance.

8. Genetic variance: definition and components Genetic variance is a measure of the dispersion of the observed average phenotype among all individuals with the genotype in question in the entire population, around the expected (average) value. Components: it is calculated by the addition of additive, dominance and interaction (or epistatic) genetic variance

9. Define “environmental variance” Environmental variance a measure of the dispersion of the environmental effect specific to the observed individuals around the expected (average) value.

10. Common-garden experiment Common-garden experiments involve the comparison of genetically distinct strains, families, or populations under identical environmental conditions. Such experimental protocols are often used to disentangle the effects of genetic and environmental variation on the phenotype. In this experiment, it is just known that the genotypic groups differ, but we don’t know the actual genotypes. It determines broad-sense heritability and the percentage of environmental vs. genetic effect on phenotypic variation.

11. Broad-sense heritability vs. narrow-sense heritability Broad-sense heritability HB = VG / VP

Narrow-sense heritability HN = VA / VP

- Not a species-level characteristic

- The variability that can be passed on

- Applies to one population at a time.

from parent to offspring. - Determines amount of phenotypic evolution caused by selection.

12. How to estimate narrow-sense heritability Using HN = VA / VP Or by breeder’s equation: R = hN2 s

13. What traits should have low narrow-sense heritability? A continuously varying (quantitative) trait whose variation is mostly or entirely environmental and the imposed selection produced NO change in allele frequency across a generation. (s > R)

14. Difference between natural selection and evolution Evolution - A change over time in the proportions

Natural Selection - Natural selection is a process in which

of individual organisms differing

events that happen to individuals alter

genetically in one or more traits in

the collective properties of populations.

order to alter the frequency of one or more genes over many generations.

- A mechanism of adaptive evolution.

- A change in genetic composition of a population over time. 15. Distinguish between stabilizing, disruptive and directional selection - Disruptive selection favors both extreme phenotypes. - Directional selection favors one extreme phenotype, reduces genetic variance. - Stabilizing selection favors the middle phenotype, reducing the phenotypic

variance by reducing the genetic variance.

16. Definition of selection differential and selection gradient as measures of natural selection - The selection differential (s): quantifies directional selection, the difference between the phenotypic mean of the selected group and the mean of the whole population before selection.

- The selection gradient (β): slope of regression of relative fitness on the trait (W relative).

The relation between selection differential (s) and selection gradient (β):

17. Response to selection: definition and how to calculate - Response to selection (R): the actual change produced in the subsequent generation – this represents actual evolutionary change over one generation.

- It is the difference between the phenotypic mean of the population in the next generation (the progeny of the selected group), and the mean of the whole population before selection.

“Breeder’s equation”

18. Genetic correlation - Genetic correlation: occurs when selection on one alle also causes an evolutionary response in another allele. Example of positive genetic correlation: the genetics that make trait A larger tends to occur with the genetics that makes trait B larger. - Genetic correlation is caused by pleiotropy (single locus affects 2 or more traits) and linkage disequilibrium (alleles affect the traits). - Genetic correlation causes correlation evolution. Correlated evolution occurs when selection on one trait also causes an evolutionary response in another trait.

19. Define correlated evolutionary response to selection. Give 2 examples discussed in class. - Correlated evolution: occurs when selection on one trait also causes an evolutionary response in another trait.

- Examples: 1)Silver fox (‘domestication’ + ‘social cognitive ability’ = direct positive selection) 2) Medium Ground Finch (‘body size’ + ‘beak size’ both grew after drought event)

20. Methods for studying adaptation - Measure selection * Which traits are positively correlated with fitness * Tells us only about current natural selection - Experiment * Controls many variables - Prediction: what is optimal? * Often a mathematical variable. * Example: leaf area in particular environment; foraging behavior - Comparative method * Many taxa or population * PICs

21. Give example of adaptive explanation that turned out to be mistaken -Explanation: adaptations evolve because the alleles encoding them outreproduce the alternative alleles. -Problem: explanation often too easy!

22. What is character displacement? Definition:

One species causes character evolution in another because of competition. Example: Native: medium ground finch, Geospizafortis New arrival: large ground finch, G. magnirostris Compete for seeds, especially large

23. Method of Phylogenetically Independent Contrasts (PICs). PICs: * To use phylogenetic information (and an assumed Brownian motion like model of trait evolution) to transform the original tip data (mean values for a set of species) into values that are statistically independent and identically distributed. * To use phylogenetic information to study if the evolution of one trait is correlated with the evolution of a second trait by focusing on the differences between taxa that are descended from a common ancestor (rather than on the trait values themselves).

24. The 2 kinds of sexual selection distinguished by Darwin - Male-male competition - Female choice

25. Pre-existing sensory bias and example - Sensory bias: female sensory preferences are a side effect (pleiotropic effect) of sensor evolution that has evolved for other reasons. Thus, there is selection on males to display these characteristics. - Example: Common Grackle’s ( Quiscalus quiscula) auditory preference of songs.

26. Sex-role reversal: example and importance to sexual-selection theory - Example: Pipefish and seahorses

* Males offer the parental care through placenta-like attachment * Males have brood patch or pouch * Males give birth 2-6 weeks after fertilization - It affects sexual selection theory because… * Females are now larger than males and have attractive traits. * Males are choosy and have preference. * Males are now have more reproductive success than females because their number of offspring is only limited by brood NOT by number of mates.

27. Rate-of-living theory of senescence The rate-of-living theory states that higher metabolism causes faster aging, which means that organisms with high metabolism live fast and die young. In other words, it is the correlations between metabolic rate and aging rate.

28. Antagonistic-pleiotropy and mutation-accumulation theories of senescence Antagonistic pleiotropy hypothesis: Alleles beneficial early in life but harmful later in life should increase in frequency.

Mutation-accumulation hypothesis: Mutations decreasing early fitness are more efficiently removed from a population than those decreasing late fitness. Thus, late-acting deleterious mutations accumulate in a population more than early-acting mutations. ( In other words: Late-acting, deleterious mutations in a population are commoner &/or have larger effects than earlyacting mutations.)

29. Aging, cancer and p53 p53 is a tumor-suppressing gene (transcription factor) activated by telomere shortening (happens more as we age) and oxidation. Evolution has set an optimal amount of p53 in individuals, and in normal p53 activity, there is a balance between longevity and cancer resistance. * Increasing and decreasing p53 BOTH reduce survival.

What is inbreeding depression? What are its genetic causes? What does an increase in inbreeding depression with age indicate about the evolutionary theories of aging? - Inbreeding depression: is the decreased average fitness of inbred compared to outbred progeny. - Genetic causes: 1) Recessive or partially-recessive deleterious alleles. 2) Overdominance. - Increasing inbreeding depression with age means that inbred offspring perform relatively worse than outbred with age.

30. What is a tradeoff? Give 3 examples that we’ve discussed in class. - A trade-off is when a choice must be made between multiple things, where an increase in one thing might lead to a decrease in another. - Examples: * The classic size-number tradeoff. * Female flower size (begonia) (negative relationship between flower number and size to increase fitness) * Trichome and Glucosinolate in Arabidopsis

31. Lack model: what does it propose? What does it assume? - Lack’s model proposes that the optimal number of offspring for each bird species’ individual corresponds with the largest number of offspring that the parents can provide food for, based on this equation: Parental fitness (or number of surviving offspring) = survival probability x clutch size

- It assumes that all offspring are the same size. *Note: this model predicts the optimal number of offspring only.

32. Smith-Fretwell model: what does it propose? What does it assume?

- The Smith-Fretwell model proposes that, as offspring size goes up, survival of any individual offspring should go up. However, the increase will eventually slow down. - It assumes that: * There is a trade-off between size and number. * Larger offspring are more likely to survive. *Note: this model predicts both the size and number of offspring.

33. Species concepts: biological, phylogenetic and morphospecies. Give an example where all three concepts agree.

Definition

Advantages

Biological Species Concept (BSC)

Phylogenetic Species concept (PSC)

A species has integrity and is unique as long as it’s interbreeding and maintaining barriers from other species.

A species is a group whose members are descended from a common ancestor and who all possess a combination of certain traits. This group does not have sub-groups (so it must be monophyletic).

A species is defined by its phenotypical differences.

- Testable (statistical significance of tree)

- Widely applicable.

- Hard to say where to stop splitting. - Proliferation.

- Vague meaning. No particular threshold of difference. Don’t know which traits. - Don’t know how testable. - Reproductively isolate groups can look alike (fungi, bacteria, archaea, many eukaryotes)

- Lack of gene flow (due to reproductive isolation [interbreeding]) - Testable - Defines research program Disadvantages - Difficult to apply when populations don’t overlap. - Does not explain asexual organisms. - Impossible to apply to fossil forms.

Morphospecies Species Concepts (MSC)

An example of when all 3 concepts agree: Marine phytoplankton (Pseudo-nitzschia)

- Originally, scientist thought there well only 2 species. - After applying all 3 concepts, it was agreed that there are actually 8 species!

34. When does the biological species concept not apply well? On asexual organisms (bacteria, archaea, some eukaryotes) because asexual reproduction has no interbreeding.

35. Difference between allopatric, sympatric and parapatric speciation (or genetic divergence) Allopatric Speciation Speciation that happens when two populations of the same species become isolated from each other due to geographic changes.

Sympatric Speciation Speciation that occurs when two groups of the same species live in the same geographic location, but they evolve differently until they can no longer interbreed and are considered different species.

Parapatric Speciation Populations that are next to each other evolve into distinct species while maintaining contact along a common border.

36. Definitions of polyploidy, allopolyploidy, autopolyploidy, tetraploidy

Polyploidy Change in the number of chromosome sets (n, 2n, 3n, 4n…)

Alloploidy Having chromosome which are composed of more than 2 genomes, each of which are from different species.

Autopolyploidy Having chromosome which are composed of more than 2 genomes, each of which are from the same species.

Tetraploidy Having four sets of chromosomes (4n).

37. Give examples of premating reproductive isolation in plants. In animals. Examples of premating isolation: * In animals: 1) Ethological premating isolation in fireflies 2) Mechanical premating isolation in snails * In plants: 1) Premating isolation from pollinators in Cardinal Flowers (Lobelia cardinalis)

38. Give examples of postmating reproductive isolation in plants. In animals. Examples of premating isolation: - [Animals] Sperm dying in female reproductive tract. - [Plants] Pollen/sperm dying in stigma or style.

39. How do populations become separated geographically? 1) Through allopatric speciation, as the species create a reproductive isolation.

2) Via polyploidy, as it creates reproductive isolation with parental species. More common in plants.

40. What are the possible outcomes of hybridization between newly diverging species? There are 3 outcomes… Reinforcement Hybrids are less fit = selection against forming hybrid zygote - Always include prezygotic isolation. - Forms 2 species.

Favoring hybrids in new habitats

Hybrids fittest only in transitional habitat

The habitats should be lacking - Forms 2 species with hybrid parental species. zone. - Forms 3 species -> homoploid hybrid speciation.

Example: Phlox and Drosophila

41. Does speciation often involve adaptation to different environments in the two groups? If so, what is the evidence? Adaption (or “Ecological Divergence”) has a positive causal relationship with reproductive isolation, which leads to speciation.

Evidence: Funk et al. (2006) study on angiosperm. 70% of the results, where ecological divergence was controlled, stated that the correlation is positive.

42. What is reinforcement of reproductive isolation? Does it apply to premating or postmating reproductive isolation? Why? Name some evidence for reinforcement. Reinforcement is an outcome of hybridization between newly forming species. It is a selection against making hybrid zygotes (applies on premating reproductive isolation) when hybrids are less fit, and it forms 2 species. Evidence: Drosophila.

43. What is special about the Cambrian Period? When did it begin? Cambrian period: 543 to 495 million years ago. Special feature: The first large and morphologically complex animals appeared in the fossil record after the explosion that happened in the Cambrian period.

44. How does the probability of extinction of subgroups within larger groups change over time? The probability of extinction within any subgroup is always constant.

45. Mass extinctions Mass extinctions are extinctions that have wiped out a large portion of the Earth’s life. - It must be global in extent and it must wipe out a significant fraction of life on Earth. - There are 5 big mass extinctions along the eras throughout history. - ...