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Final Exam Study Guide

by: Sarah Doberneck

Final Exam Study Guide GE 70B

Sarah Doberneck

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This study guide includes the review questions and answers from both halves of the quarter, as well as lecture notes from the second half of the quarter to help with clarification of some of the co...
Evolution of Life and the Cosmos
Dr. Friscia
Study Guide
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This 46 page Study Guide was uploaded by Sarah Doberneck on Saturday March 12, 2016. The Study Guide belongs to GE 70B at University of California - Los Angeles taught by Dr. Friscia in Winter 2016. Since its upload, it has received 105 views. For similar materials see Evolution of Life and the Cosmos in General at University of California - Los Angeles.


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Date Created: 03/12/16
Final Study Questions 1. Discuss some advantages and disadvantages of asexual versus sexual reproduction.  Asexual reproduction doesn’t take the same amount of energy to find a mate like sexual reproduction does  Asexual reproduction results in less genetic diversity. Every offspring is passing on 100% of your genes. Relatedness is considered an advantage because of this  sexual reproduction however could also been seen as having the advantage of increased diversity and  asexual populations=no stds  asexual reproducing organisms would have to evolve independently whereas sexual reproducing organisms cans spread these advantages and evolve quicker  sexual reproduction means bad alleles are more quickly purged  Muller’s ratchet- bad mutations accumulate 2. What is Bateman’s Principal? Make sure you understand the rationale behind it.  Females put much more energy toward reproduction, from just making the egg with all the lipids and stuff along with either gestation or child care that the male doesn’t have. So females don’t want to just mate with the first male they see they are very choosy, and males have to make themselves sea like the best mate  in seahorses, the males are responsible for child care so this isn’t true in that case  with goby things the males guard the nest so this isn’t trey in that case either 3. What is parthenogenesis and how does it happen? a. Can be cloning but sometimes isn’t the same as cloning b. It’s when females produce eggs that form into fully developed organisms c. Meiosis will occur twice, causing a doubling of chromosomes then only have of them actually are used. This is how the offspring isn’t an exact clone and has some genetic diversity 4. Give a detailed example of how natural and sexual selection might oppose each other a. Females might choose a male with a trait that doesn’t benefit his survival or even hurts his survival b. Female peacocks like males with very large and extravagant tails, but they sometimes become so big that they hinder the birds ability to flee from predators when they need to c. Another example could be 5. Describe the role of male and female traits in Fisher’s theory of runaway selection. a. Males have variation, and females get a mutation where they prefer a certain trait for whatever reason. Example would be females who prefer red tails for mates, so males with red tails get more mates and pass on the red tails to their sons and the daughters get the preference for the red tail from their mothers b. It doesn’t just stay in the paternal or maternal lineages. The daughter can inherit the male tail gene although she doesn’t express it c. runaway selection occurs when this becomes more and more extreme until it causes a disadvantage survival wise 6. Describe the Red Queen hypothesis as it applies to sexual reproduction. a. It is an arms race between host and parasite b. The parasite has a way to kill the host, the host develops a resistance to it c. the parasite catches on and then suddenly having that trait that was useful is no longer helpful d. so being rare is the best thing because it means you have an advantage e. each side just keeps going up and down and there is no winner f. reciprocal selection between host and parasite but selection meant genetic drift could work well in some and not in others because of the randomness of alleles g. drift is always going on but it has a much bigger effect when the population is small because there are less cards being passed out 7. What is sperm competition? Is it most likely to occur in polygynous or polyandrous mating systems? Why? a. Sperms compete against each other to fertilize the egg b. it’s a portion of fitness because the male with the most and strongest sperm are going to get there faster c. more likely in polyandrous because there are multiple males sperm in the females reproductive tract d. seen by looking at apes and ones that were part of polyandrous mating systems had bigger balls e. polyandrous were longer and had spines, non-polyandrous were smaller and simpler 8. How does frequency-dependent selection work in side-blotched lizards? a. Orange, blue, yellow lizards b. orange are the most aggressive and get the most mates c. yellow can sneak into the orange territory and mate with the females d. blue keeps yellow in check e. 9. Name the two major species concepts and describe each one. a. Phylogenetic b. Biological 10.Why is the ability to breed not sufficient as a general rule for recognizing distinct species? a. Asexual reproduction b. Inbreed can be successful 11.Describe problems with both the Biological and Phylogenetic Species Concepts a. 12.How did the rise of the Isthmus of Panama affect marine and terrestrial species differently? Land bridge between north and South America Isolated the marine taxa and we know when they diverges, we know what things were species before and after and see ow they evolved independently 13.Compare and contrast pre- and post-zygotic isolation. Pre is when they don’t mate in the first place because they are separated Post occurs when they mate but their offspring aren’t fit, hybrids are less fit so that creates reinforcement 14.Compare and contrast allopatric and sympatric speciation. a. Allopatric; they are separated and mate on their own for long enough that their genes aren’t compatible anymore b. Sympatric: different mating seasons, host shift, etc. make them incompatible 15.Why is reproductive isolation important for origination of new sexually reproducing species? a. 17. What is reinforcement and how might it occur following secondary contact? **Week 7** 1. What are the different predictions made by phyletic gradualism and punctuated equilibrium for what we should see in the fossil record? a. Phyletic: expect to see transitional forms b. Punctuated: no transitional forms 2. Why is the Burgess Shale such an important fossil locality? a. There is a good record of hard and soft parts from organisms. Normally soft parts aren’t fossilized b. Had the first record of a lot of groups including vertebrates including humans c. Cambrian explosion, huge increase in life where we get a lot of hard parts all at once 3. What are some arguments for and against the Cambrian Explosion being a real 'explosion' of life? a. For: climatic change may have contributed to an increase, increase in complexity in life driven by the 3 germ layers,, appearance of predators and a food pyramid b. Against: there may not have been as many new species as we have thought. Things we thought were knew were actually around for a while before then but we don’t have a good record. It might look like an explosion because the fossil record got a lot better, trace fossils like burrows from before that 4. Name 2 things that Sepkoski showed in his graph of marine diversity across the Phanerozoic. a. Increase in diversity b. pull of the recent is an artefactual thing because we know more about things more recent c. could also be a real thing of ecological diversity d. mass extinctions- big 5 5. What are two possible explanations for the increase in marine diversity across the Phanerozoic? a. 6. What defines a mass extinction? a. Global b. affect marine and terrestrial organisms c. happen fast 7. Describe the trade-off that tends to prevent parasites from quickly killing their hosts. a. Virulence: high virulence means they are good at spreading and infecting the host b. too high of virulence and they end up killing the host or disabling him from moving around before they can transit to the next host means that they failed 8. What is Symbiodinium and how is its existence important for reef-building corals? What is coral bleaching? a. Single celled organisms algae b. their waste products are food for each other- algae gives photosynthesis products (normally coral reefs eat plankton but there isn’t enough nutrients from plankton or enough of it to survive) and algae provides CO2 and shelter c. coral bleaching is the coral in stress and this happens usually from increase in temperature, even 1 to 2 degrees warmer can cause the corals to bleach d. If the algae doesn’t recolonize quick enough the coral with also bleach and die e. This is an example of mutualism 9. Why is species interaction a necessary component for coevolution to occur? Why don't ALL species interactions lead to coevolution? a. Species interaction is necessary because they need to interact for there to be a reason to evolve together b. They need to directly cause evolution in the other species and vice versa 10.What is meant by a mosaic of coevolution? a. Two coevolving species that have a relatively high range, and the effect that one species has on another is not constant throughout that range b. In areas where garter snakes eat a lot of newts with little other options, the newts are probably going to be more toxic c. in places where there are newts and garter snakes but snakes have more options, the newts probably aren’t that toxic 11.Describe parasitism, commensalism, and mutualism. Give a specific example of each that was NOT presented in lecture. a. Parasitism: one organism harms another for its own benefit (dogs and fleas) b. Commensalism: interactions benefits one species, little to no effect on the other (ex: ) c. Mutualism: interaction that has a positive effect on both species involved (pollination, seed dispersal) 12.Compare and contrast Müllerian and Batesian mimicry. a. Mullerian: two unrelated toxic animals look alike (convergence) and strengthen the idea that they’re toxic because the population size is combined b. Batesian: one is toxic, another species gets that same coloring symbol when they aren’t toxic. For this to work the nontoxic must be rare or it’ll all be screwed up 13.Describe how coevolution can facilitate both speciation and extinction a. Speciation: generates diversity that can lead to different species forming b. extinction: they become too dependent on each other so if one of them starts to die, then the extinction of the other happens c. flowers relied on birds to spread their pollen, those birds either died or moved away so the flowers couldn’t reproduce **Week 8** 1. Describe how sponge larvae may tell us something about the origin of animal neurons. a. They can sense their environment and respond to it b. This is only in the embryo not in adult sponges 2. Why does our typical understanding of behavior present problems when studying plants? a. Watch the nyt video about plant behavior b. They don’t have neurons and they just don’t do anything the way that we do it. The things we have studies with animal behavior is in a totally different context c. They might be responding to their environment in ways we don’t appreciate because they grow slowly and we can’t always see it 3. Compare and contrast instinctive versus learned behavior. a. Instinctive: has a genetic basis b. Learned: trial and error, eat something oh that’s not good I won’t eat it again 4. How was the ability to learn selected for in Drosophila fruit flies? Make sure you understand how this was distinguished from instinctive behavior. a. The ability to learn which jelly was gross b. They didn’t detect the bitterness until they tried to eat the jelly, then they would stop eating the gross one. Scientists picked out the quickest learners and bred them and the flies learned faster c. switches the jelly flavor that was the gross one so they didn’t just pass on that grape was the best d. the tradeoff was the flies that learned quicker also died sooner 5. Explain, in detail, how altruism in non-reproductive female worker bees can be evolutionarily stable. a. Female worker bees are all diploid, b. Each have 75% relation between sisters, so the one sister that becomes the queen and reproduces ends up passing on a lot of the genes so the sisters are all focused on keeping the hive healthy and reproducing 6. What does the term green beard mean? Give an example. a. it is about behavior an altruism and preventing cheaters b. predicts bearers of a trait will behave better toward others with the same trait c. There’s genetic linkage between social behavior and signaling trait d. Requires honest signaling (Having a green beard means you are a cooperative individual) 7. Describe how slime molds exhibit a very primitive form of altruism. a. When it’s time to reproduce, they form together into slugs and create a stalk that allows the ones on top to reproduce but the bottom ones don’t b. If all the individuals wanted to be on the top, no one would get there because there wouldn’t be anything to stand on c. The individual cells recognize which individuals have the green beard and all work together. Ones without the altruistic gene don’t get included in the reproduction party 8. How might a runaway greenhouse effect have occurred at the end of the Paleozoic and contributed to the mass extinction then? a. Greenhouse gases released from volcanism could cause global warming. This would raise sea temperature and land temperature an cause the melting of methane hydrates, which would also cause more warming and cause a runaway greenhouse earth b. This release in CO2 would mean a decrease in O2 and more acidic waters, killing plants and animals form this time 9. What are some lines of evidence for the meteor impact at the K/T boundary? a. Iridium spike not common on earth b. crater dated to this time 10.How can a sudden extinction look like a gradual extinction in the fossil record? a. The fossil record is spotty to begin with b. Things might have died all at once but become fossilized gradually 11.What is the fossil record of primates prior to the evolution of apes? a. Prosimians b. anthropoids c. old world new world 12.What are the main differences between humans and apes? When, where, and in what taxa did these differences first appear? a. Upright walking, big brains b. Upright walking comes first, group is alstropithecenes c. Bib brains are in homo d. Happened in Africa about 5 to 7 million years ago 13.What are some adaptations to walking upright in humans? a. Narrow and shortened pelvis b. Hole in skull that points down so the skull sits on top of the vertebrae c. Reduced curvature of fingers and apposable big toe Terms and taxa to know: Prosimians: primitive living primates Anthropoids: modern higher primates, can be divided into the Old World monkeys, New world monkeys, and apes Darwinius: the most complete fossil primate ever found, he is 47 mya. The fossil shows hair stomach contents and sex. He is very near to the origins of anthropoid primates Kamoyapithecus: the earliest ape. Found in the Miocene of Kenya, 24 mya. Agrees with molecular divergence times of apes and old world monkeys Apes: part of the anthropoids tree, they are still around. Humans are evolved from apes Ardipithecus- earliest australopithecines Australopithecines: existed from about 5-1.5 ma, less than 4.5 feet tall. Bipedal apes with chimp size brains, good climbers. Earliest hominids Hominids-lead to humans. Had to move across the ground instead of through trees, had to get bigger brains so they could think to defend themselves, their hands were now free from walking upright allowing them to take care of their children. Said to move away from polygamy to monogamy **Week 9** 1. How do Neanderthals fit into the story of human evolution? a. Separate sub species of homo sapiens b. evolved from homo erectus c. they added to the modern human genome d. We can see bits of Neanderthal genes in modern humans 2. How are upright walking, childbirth, and big brains related? a. As we started walking upright we got smaller birth canals and an increase in brain size that made it harder to pass a baby through the birth canal because of its fat ol head 3. How did a change in our reproductive pattern affect the way we grow? a. Our adult faces look like the faces of the juveniles of our ancestor b. we are helpless when were born 4. What's different about the way dogs and cats grow? a. Dogs change shape a lot more as they grow, so we have more breeds of dogs then we do cats b. This allows for breeding that selects for more juvenile traits c. Dogs grow allometrically cats grow isometrically 5. How does the evolution of humans relate to sex? a. Safety, food, reproduction b. in humans, the upright walking allowed us to put more energy into reproduction because when the males and females cooperated they could have more babies and the dad would bring food back to the offspring c. the caveat is that the male needed to know that the baby was his and he was working toward making sure his genes get passed on d. led to monogamy, reduced outward signs of ovulation 6. Explain the physical basis for the greenhouse effect. What are the most important GHG and why? a. part of the Earth’s outgoing thermal radiation is captured by some atmospheric constituents (GHGs) like H20, C02, O3, etc. (present in trace amounts with respect to N2 and O2); b. greenhouse gases act as a blanket; thanks to this phenomenon life is cozy down here; c. so the greenhouse effect is a naturally occurring phenomenon helpful to life on Earth 7. How has the concentration of CO2 varied over the last (a) 50 million years, (b) thousand years, (c) two centuries??  much higher increase right now and its directly connected to burning fossil fuels  50 million years ago there was variation  thousand years ago was a mini ice age so it wasn’t as much of a change  two centuries its increasing a lot and its increasing fast af 8. What specific evidence is there that the climate is warming over the last century? a. Rising sea level, melting ice b. Geological record shows the increase in temperature an dCO2 over the years, and has experienced far warmer times but these times were spread out over many more years and what’s happening now is very rapid 9. What evidence is there as to the cause of the warming? a. Well it’s not the sun because temperature has been increasing over the last 35 years while solar activity is increasing b. Fluctuations of temperature and concentration of carbon dioxide follow each other until recently when they both rise very suddenly c. The geological record contains evidence that natural increases in CO2 concentration d. Also caused by the burning of fossil fuels and methane 10.How is carbon transferred from slow to fast geochemical cycles (and vice- versa)? a. The fast carbon cycle is largely the movement of carbon through life forms on Earth or the biosphere. Plants and phytoplankton are the main components of the fast carbon cycle. Most photosynthetic energy is consumed in the biosphere, either by plants and animals or by bacteria during decay following organism death. The timescale is from months to 1000s of years b. The slow carbon cycle takes 100 to 200 million years and is when carbon moves between rocks, soil, ocean, and atmosphere c. Some biomass can be sequestered in environments where it is not easily oxidized. Under some PT conditions, oxygen can be removed from the carbs producing reduced organic matter. If they are concentrated, trapped and then extracted, they are fossil fuels (petroleum, natural gas, coal) d. Combustion is the rapid reaction with oxygen, the energy released is ultimately derived from photosynthesis 11.What data are used to infer climate conditions? Can you name a couple of data sources? a. Atmosphere and ocean have warmed, amounts of snow and ice have diminished, sea levels have risen, and the concentrations of greenhouse gases have increased b. These observations are all unprecedented 12.Why is sea level expected to rise in the next 50 years? a. Scientists expect that the average global surface temperature could rise 0.6-2.5°C in the next 50 years, and 1.4-5.8°C in the next century, with significant regional variation. Evaporation will increase as the climate warms, which will increase average global precipitation. Soil moisture is likely to decline in many regions, and intense rainstorms (hurricanes?) are likely to become more frequent and/or more powerful. Sea level is likely to rise two feet along most of the U.S. coast. Terms and taxa to know:  Homo erectus: the first hominid to leave Africa and enter Europe/Asia, first to leave evidence of stone tools  Heterochrony:   defined as a developmental change in the timing or rate of events, leading to changes in size and shape. There are two main components, namely (i) the onset and offset of a particular process, and (ii) the rate at which the process operates.  Paedomorphosis: The evolutionary process in which larval or juvenile features of an ancestral organism are displaced to the adult forms of its descendants. It can arise by neoteny or progenesis.  Allometry: a change in the rate of growth of a dimension or feature relative to other features.  Isometry: all the body parts grow at approximately the same rate, and the adult proportions are not significantly different from those of the juvenile **Week 10** 1. What is the Drake equation? a. Number of civilizations=Nstars x fhp x flife x fciv x fnow b. Nstars = number of stars in the Galaxy c. fhp = fraction of stars with habitable planets d. flife = fraction of habitable planets where life develops e. fciv = faction of life-bearing planets where a civilization arises fnow = fraction of civilizations which exist no f. -evaluates the number of civilizations in the galaxy we could make contact with 2. Which types of stars are considered the most likely to host habitable planets? a. Goldilocks thing with not too close to the sun not too b. -they must be old enough so that life could arise (possibly a billion years) c. -they must allow for stable planetary orbits d. -they must have relatively large habitable zones (surface temp where water could exist) 3. What are the techniques we discussed that an interstellar spaceship could use to travel to a nearby star? What are the typical timescales for this travel? a. fusion power- dropping fusion bombs out the back to push the spaceship b. fission- nuclear power c. timescales for this travel are in centuries 4. The sun is moving relative to nearby stars. Why does this make it even more difficult to explain why no aliens have ever made their presence known? a. we are constantly changing neighbors and many get close enough to be detected with life detecting telescopes 5. What is Fermi’s paradox? What are some of the possible solutions? a. there are suns like ours that are 5 billion years older meaning they could've been colonized, so where are the aliens? b. -we are alone c. -others don't feel the need to colonize or communicate d. -they try to keep themselves hidden Midterm Review Questions 1. What are the premises of natural selection? a. Individuals vary within a population (no two individuals are exactly the same) b. More individuals are produced than can survive c. The variation influences the survival and reproduction of individuals (some will  do better than others, i.e. natural selection d. If the variation in features is heritable, there will be evolution 2. How are ecology and evolution related? a. Ecology is interactions of organisms with each other and their environment.  Evolution is the reaction to ecology­it gives depth of time to ecology and links  organisms via genetic information and shared ancestry 3. What are some lines of evidence for evolution that can be seen in the evolution of  whales? a. Direct observation b. Comparative anatomy c. Classification d. Comparative genomics e. Fossil record (paleontology) f. Biogeography g. Embryology/development 4. What were the molecular and morphological hypotheses about whale origins?  What  resolved this discrepancy? a. Whales were thought to be from an organism known as Mesonychia based on  fossil record. By looking at the DNA of living whales and comparing that to other organisms, it was shown that by looking at just their DNA their closest living  relatives are hippos. The fossils show that whales were outside the group of  hoofed animals that included hippos. The morphology told us that whales were  not included in the group of even hoofed animals (zebras, camels, cows, etc.) and  the DNA told us that they were inside the group. One of the key things that links  them all together is a special bone in the ankle that allows them to run. WE never  had found ankle bones for whales at this time, but an expedition to Pakistan found a whale ankle bone that looked a lot like the hoofed mammals, which confirmed  that they could be inside the group.  5. What is the difference between homology and analogy? a. Homology: derived from a common ancestor, but not necessarily similar in form b. Analogy: similar in form, but not derived from a common ancestor­ due to  convergence 6. What are some unique cetacean characters? a. They have a blow hole, moved their nostril from the front of their nose to the top  of their head b. Reduced pelvis and hind limbs c. Modified their ears to have the ability for echolocation 7. How are vestigial structures explained by evolution? a. They are characters/parts with no apparent function, but must have been  functional to our ancestors and persist in reduced form if they are not harmful. 8. Why are early whale fossils found in India and Pakistan? a. The answer lies in plate tectonics. At the time whales were evolving, India hadn’t  smashed into Asia yet and there was a shallow sea between India and Asia with  fresh water rivers flowing into it.  This is the area where whaled evolved, in these  fresh water environments. These areas were pushed up and made in to the  Himalaya Mountains.  9. How can development (i.e., ontogeny) inform us about evolution? a. early embryological stages reveal something about our ancestry ex. Humans early on have gills, something that shows we come from fish 10. Name two individuals and/or cultures who had thought about evolutionary change prior  to Darwin, and describe their ideas. a. Lucretius­ earliest expression of "survival of the fittest," every species today  survived through being more advantaged than others b. Lamarck­ believed evolution occurs gradually through the use and disuse of  structures/traits 11. Describe how the economist Thomas Malthus inspired Darwin to formulate his theory of  evolution by means of natural selection. a. Malthus noted that organisms produce more offspring than can survive due to  resource limitations. This led Darwin to understand the relationship between  struggle for existence and how variation can produce evolution. 12. Explain how Lamarck was right about evolution, and how he was wrong. a. he was right about species inheriting acquired traits but believed that evolution  was driven towards complexity, when it has no set path 13. What various observations and lines of evidence did Darwin bring to bear on the topic of  evolution? a. Darwin added the ideas of natural selection, population thinking, and chance to  the theory of evolution. Deep time, uniformitarianism, artificial selection. He tied  all the ideas together. 14. What is a 'straw man' argument?  Give an example of one used against evolution. a. create a false premise, then beat it up to make yourself look credible b. Ex. if humans came from apes then why are there still apes? 15. Describe two common misconceptions about evolution and how they are wrong. a. Evolution doesn't explain the origin of life. This is true but irrelevant, because  evolution explains how life has changed SINCE origination! b. The human eye is too complex to have evolved randomly. Evolution is not  random, MUTATION is random, and natural selection only occasionally favors  certain mutations determined by their environment. c. If evolution is true, why aren't there transitional fossils? There are literally  THOUSANDS but we just can't find them all, even though we've found a bunch.  Moreover, fossilization is very rare so a lot of creatures didn't fossilize or are  buried too deep underground. Week 2 1. What are some developments in the history of biological thought that occurred after  Darwin? a. Mendelian inheritance, the discovery of DNA, Modern Synthesis, Neutral Theory 2. What were some things that Darwin got wrong, and why did it take so long for his ideas  to catch on? a. Age of the Earth, mechanism for inheritance (pangenesis). It took a long time for  his ideas to catch on because there were no transitional fossils and difficulty of  evolving complex structures.  b. Moreover, there was a strong Christian idea that things don't change, and this was  strong for a long time. He waited awhile to publish because he knew there'd be a  lot of controversy. 3. What are some different types of fossils? a. Fossils are all evidence of past life b. whole body fossils c. mummification, frozen and bog specimens, amber d. preservation of hard parts and petrification e. molds and casts f. trace fossils (ichnofossils) g. chemical traces 4. What happens to an organism from the time it dies to the time it's exhumed as a fossil?  What is the study of this process called? a. Taphonomy is the study of the processes by which animals become fossilized. They  go through consumption and decomposition, exposure and weathering, transport and  burial. then fossilization and exhumation 5. What is 'uniformitarianism'? a. Concept of “Deep Time” – large amounts of time and recurring processes can  account for the observations we make today  b. “Present is the key to the past” – (only) events that occur today also happened in  the past  c. Opposed to Catastrophism/Neptunism – One large event (a flood) account for the  geologic features we see 6. What are some rules for determining relative ages? a. superposition: older rocks are under younger rocks b. Original horizontality: rock layers are originally deposited horizontally. folded  beds indicate deformation c. cross cutting relations: older rocks may be cut by younger rocks or other  geological features d. Included fragments: if fragments of one material are included in another, then the  included material must be older. All clasts in a sedimentary rock must be older  than the rock in which they are now found 7. What are index fossils and what are they used for? a. index fossils of a particular age are used to correlate between strata of the rock  layers must be easily distinguishable, widespread, alive for short periods of  geologic time, abundant b. called biostratigraphy 8. How long ago did life start? What is some evidence of this early life? a. the oldest record of life is from 3.5 billion years ago b. Miller­Urey experiment simulated the conditions thought to be present on early  Earth and tested the chemical origin of life. Other evidence is banded iron  formations and carbon isotope change. Plants prefer C12, with more life the ratio  C12/C13 goes up b/c more C13 in atmosphere 9. Give the dates for the following time spans: Paleozoic, Mesozoic, Cenozoic, and  Phanerozoic. a. Paleozoic/Phanerozoic: 550Ma b. Mesozoic: 245 Ma c. Cenozoic: 65 Ma d. Phanerozoic spans to present! 10. Define the following terms and give examples: heterotroph, autotroph, eukaryote, and  prokaryote. a. Heterotroph­ An organism that consumes carbon for growth, like humans b. Autotroph­ An organism that can supply power for its own growth, like plants c. Eukaryote­ Multicellular organism. Nucleus with DNA, mitochondria, larger,  have internal membranes. An example is plants. d. Prokaryote­ Unicellular organism. Free­floating DNA, very small, no organelles  or cytoskeleton. An example is E. coli 11. What does it mean to say that a phylogenetic tree is a hypothesis? a. We want to know how a species evolved, but we have to only look at one  characteristic to do this. You can use DNA or morphology and each might have a  different order of things or be completely different b.  Convergent traits are a problem in morphological trees because they trick you  into thinking they are related when they're just similar. Instead we want  homologous traits  c.  Shared and derived traits provide the real information  12. What is a paraphyletic group and why is it important to understand what it is? a. A group of ancestors plus it's descendants b. Does not normally include all descendants however c. One example is with the reptile paraphyletic group which doesn’t include avian  descendants because when they were grouped it was not known that birds were so closely related to reptiles 13. Describe the difference between derived & ancestral characters. Which are more useful  for understanding phylogenetic relationships and why? a. Ancestral Character­ Already present in the evolutionary lineage leading up to the group in question (i.e. eyes) b. Derived Character­ Unique to the group in question (i.e. backbone in vertebrates). c. Ex. homology can be similar 14. Describe a situation where loss of a character can be informative for building a  phylogeny. a. It can unite several descendants if their ancestor lost the character. They aren't  inheriting the trait, they're inheriting the loss; still unites, but you just need more  information to be able to make sure they're related in the first place. 15. Why is it important to distinguish between homology and convergence when building a  Phylogeny? a. Homology indicates that there is a common ancestor, whereas convergence might  mean similar traits that were developed independently, not from the same  ancestor. This is important when making phylogenetic trees because it affects how they are placed and if the tree says they are related which might not be accurate if  using convergent traits.  16. Give one example of how a species might lose a character. What does natural selection  have to do with this? a. If environmental conditions make a particular trait undesirable, then that species  may lose the character. It is based completely on natural selection as the  organisms with that trait will most likely die off in the environment.  17. What’s the difference between taxonomic classification (like what Linnaeus did) and  phylogenetic (tree building)? a. Taxonomic: based on common characteristics b. Phylogenetic: based on common ancestry and homology   Week 3 1. Why is "junk DNA" a terrible name for DNA that does not code for proteins? a. Name for the 98% of DNA that doesn't  code for protein b. They actually do lots of fun things like regulate stuff and turn things on and off  and all that 2. Explain how the idea of blending inheritance created a problem for Darwin's theory of  natural selection. a. Thought that for example a small mom and a very tall dad would create a medium height child. Created a problem with the fact that characters did not get diluted  and would reappear generations later 3. Describe at least 5 different types of mutations (hint: a single nucleotide substitution is  the most simple). a. Point mutation b.  Insertion c. Deletion d. gene duplication e. inversion f. chromosome fusion g. genome duplication 4. How does an X­linked recessive allele affect men and women differently? a. Women are able to get these genes from both parents, while men only get them  from their mother. This means that if the mother has an x­linked recessive allele  then girls may not have it because they will get a dominant allele from their father and therefore not be affected by the mother’s genes, but they will still be carriers.  The boys on the other hand only have one X chromosome which they get from  their mothers, so they have the recessive allele and are affected by that gene.  5. What is pangenesis? a. This is the theory that atomic sized “gambles” carry information about the cells  they are produced from throughout the body and are responsible for reproduction.  However, there was a lack of solid evidence for this idea since traits acquired  after birth could not be passed on. (rat­tail experiment) 6. Name and briefly describe the 3 laws of Mendelian inheritance. a. The law of dominance: when both alleles are present, the dominant one will be  expressed b. Law of Segregation: every diploid individual possesses a pair of alleles for a  given trait. Each parent passes one copy to their offspring c. Law of independence: alleles for different traits are inherited independently.  Genes sort randomly and independently during gamete formation, so gametes  from one individual end up with a lot of combinations. 7. What is gene regulation and how is it important in the connection between genotypes and phenotypes? a. Gene regulation is caused by DNA that essentially turns genes on and off. It is  important in the connection between genotypes and phenotypes because even  though many species share the same DNA, the gene regulators cause the traits to  be expressed differently.  8. Compare and contrast the difference between a prokaryotic and eukaryotic genome. a. Prokaryotic genome: single chromosome, circular, free­floating DNA, small, no  cytoskeleton or organelles. Transfer DNA through horizontal gene transfer. b. Eukaryotic genome: Nucleus with DNA, mitochondria, larger, have internal  membranes, organelles 9. What are p and q, and how do they relate to genotype frequencies in a population? a. p= frequency of a dominant allele b. q= frequency of a recessive allele c. p+q=1 d. p^2(AA)+2pq(Aa)+q^2(aa)=1 10. What is Hardy Weinberg Equilibrium, and what are the conditions for it to be true? a. The Hardy­Weinberg Equilibrium is a way to find out the frequency of dominant  and recessive alleles.  b. The conditions for it to be true are: random mating, large populations (b/c no  drift), no migration, no mutation, and no natural selection. 11. How does nonrandom mating affect genotype frequencies in cases of consanguinity, and  how does this relate to fitness? a. It decreases diversity of alleles and creates more homozygotes. There is a greater  representation of harmful phenotypes and the population is more susceptible to  illness disease and death. 12. What is genetic drift, and why does it affect small populations more than large ones? a. It is random changes in allele frequency causes by limited genetic sampling b. It affects small populations because they have a smaller gene pool 13. What is a random walk, and how does it relate to genetic drift? a. The change in the proportion of alleles over time b. The comparison of a drunk man on a train having a 50% change of either dying or going home.  c. It relates to genetic drift because it gives an example of how some traits can  randomly die out or continue in a population. d. In a small population, the platform will be less wide and make it more likely that  a trait will die out. 14. What are founder effects and population bottlenecks and how do they relate to  conservation of endangered species? a. In founding populations, it is an unrepresentative sample of the original  population die to chance because it is normally very small. A population  bottleneck is when a population is about to go extinct but resurges and grows  faster than the mutation rate is able to create genetic variation. b. This relates to the conservation of endangered species because if something enters the population that can harm them, they are so genetically similar they they risk  becoming extinct/endangered once again.    Week 4 1. What's the difference between a cladogram, a phylogram, and a chronogram? a. Cladogram: only the topology (pattern of splits) is important b. Phylogram: the length of the branches represents amount of evolutionary change c. Chronogram: branch length represents absolute time. With a chronogram, you can get a RATE to calibrate the rest of the tree. 2. Describe why life­history traits can be useful for discerning evolutionary relationships  and give an example. a. If something changes a lot from larval to adult states,  you may not realize they  share similar structures to other organisms b. An example is how barnacles were thought to be related to mollusks, but by  looking at their larval characters, it was discovered that barnacles were closer to  crustaceans. 3. What was the Modern Synthesis and what fields of evolutionary study did it bring  together? a. It is a grand unifying theory of evolution that brought together biology with  natural selection, paleontology with the fossil record, and mathematics with  population genetics 4. Explain Kimura's Neutral Theory and the evidence behind his argument. a. This theory contradicted the modern synthesis and said that genetic drift is the  primary form of evolution rather than natural selection. b. Most mutations have no effect on fitness and most DNA is non coding. Therefore, if DNA doesn’t code for DNA then most mutations must be neutral and not  affected by natural selection.  c. A neutral mutation is also called a silent mutation because it has no beneficial or  hindering effects. 5. Explain why the Central Dogma doesn't explain the nature of molecular evolution as  completely as once thought. a. Brought inheritance together with natural selection b. Figured out how DNA codes for the proteins but doesn't recognize the hidden  genome, or gene regulation. It's more and more important in terms of evolution  6. Draw a 5­taxon cladogram and label one tip, one branch, and one node. 7. Explain how a phylogram can be converted to a chronogram. a. By knowing when one speciation event in a tree occurred, we can use that  information to date the other branches in the tree 8. What is meant by the term molecular clock? Why is it rarely perfect/strict? a. This is the thought that genes will change at a regular pace. It allows you to get  information about tone node by the age of another node. b. It’s rarely perfect because some genes change/evolve more quickly than others  and environment has an effect 9. How do the stories of the peppered moth and DDT resistance in mosquitos illustrate the  premises of natural selection?  What experiment from the book is the peppered moth  example most similar to? a. Peppered moth=inheritance b. DDT=variation c. Different moths have different levels of resistance to the chemical, and the ones  that are more resistant lived and created offspring that were resistant to it until the entire population was no longer affected by this pesticide d. It is similar to the experiment with bacteria who growing and getting less and less  glucose. The ones who were able to produce more of their own food needed less  glucose than others and survived longer.  10. What are some constraints on the power of selection? a. Phylogenetic history, lack of appropriate genetic variation, traits that appear post  reproductively and therefore aren’t passed down, developmental interactions  among organs or structures that necessitate trade­offs 11. What are the modes of selection, and how will they affect the variation of a continuous  trait in a population? a. Directional: when one extreme trait is most fit b. Stabilizing: when the middle of the road trait is most fit c. Diversifying: when more than one trait is the most fit, usually the extremes on  either side 12. Sickle­cell is an example of balancing selection; what does this mean? a. The best fit genes are heterozygous. SS usually die from anemia, AA have higher  mortality from malaria. AS have a little anemia and a little malaria resistance so  they survive more. 13. How are drift and selection related?  When is one or the other stronger? a. They both result in changes in allele frequency and therefore cause the evolution  of a species b. They are related in that they often oppose one another because they affect  opposite sized of populations 14. Why is gene duplication the first step in adaptation?  Give an example of this that we  talked about in class. a. Gene duplication results in mutations, which allows evolution to tinker with the  genome of a species 15. What are HOX genes? a. Genes that determine the orientation of an organisms body b. Aka they decide which limbs go where 16. How does the evolution of flippers in aquatic tetrapods illustrate that evolution is a  tinkerer? a. You can see that everything had a similar origin then slowly changed. They have  the same types of bones but form in different ways. Week 6 Lectures Asexual reproduction  Many species can reproduce without sex  Advantages to asexual reproduction  Makes adaptation difficult o Sexual reproduction can combine beneficial mutations that Aries in different lineages o Asexual reproduction Doesn't combine beneficial mutations so adaptation may take longer Send maintains genetic variation  Asexual reproduction takes inbreeding to the extreme  Millers ratchet: deleterious alleles accumulate within lineages o All alleles passed in, instead of half as in sexual reproduction o Un more difficult or impossible to purge bad alleles o Sends asexual lineage on a path to extinction  Sex shuffles allele combinations (generates new genotypes) each generation Red queen hypothesis  Sex may also provide a way to evade parasites o A host gets a mutation that exists infection, selection will increase the frequency of this allele o The parasite counters with its own mutation which then also increases in frequency o Host mutation is no longer resistant so frequency decreases o Decrease in parasite mutation follows, cycle continues  What does sexual reproduction have to do with this? o Parasite typically have much shorter generation time the hosts  Allows their populations to evolve more quickly o Sex allows the host to keep up with the parasites evolution and resistance o Evidence: snail population s in New Zealand Sexual selection  Darwin was puzzled by certain male traits that seemed to hammer survival (e.g. Large, colorful peacock feathers)  Sexual selection is the selection for a trait that increases mating opportunities. Occurs when three is competition for mates o Direct competition between individuals of the same sex o Indirect competition to n the most attractive to opposite sex  Females pit Moore energy into reproduction o Ovulation and pregnancy take a lot of energy and time  Batemans principle o Females are a limited mating resource because egg as are costly. Also the parental obligations take time. So females are very choosy and then makes have to be impressive Natural selection vs. sexual selection  Bright colors and conspicuous ornaments would seem to attract predators, how do they evolve and persist?  Runaway selection (example): o Female peacock liked a big bright tail o Sons inherit dads. Big bright tail o Daughters inherit moms preference for it o Runaway selection ensues, tails get bigger and brighter o Stops only when dangerous threshold is met  Reproductive benefit to being conspicuously sexy must be deed the cost of being more visible and vulnerable to predators  What might drive female preference in the first place? o Could be arbitrary and runaway selection would still work  As long as daughters inherit the preference, makes with preferred traits have fitness advantage o Or, attractive male traits may be a sign of vitality  Could initiate or reinforce male preference o What about liars?  The trait must have a cost. Energy is expended to attract the female using that trait and shows that the individual is healthy Monogamy vs polygamy  Monogamy: when male and female mate only with each other during a breeding season o Rae among animals o Typically arises only when care from both parents gives strong selective advantage to offspring  Females are often polyandrous to hedge their bets and make sure they are investing in good sperm o Eggs limit their production so they are more choosy o Creates direct competition between sperm o Make strategies to ensure competitive sperm  Increase quantity of sperm  Increase quality of sperm  Remove sperm of previous males  Aggregation of sperm allows it to swim faster. The sperm combines with other sperm from the same male o Makes need to get around female defenses against fertilization o One eggs. Many sperm (polyspermy) is usually bad  To prevent this, females evolve ways to avoid fertilization  E.g. Gamete Recognition proteins evolve very rapidly  Proteins on the surface of sperm must recognize those on egg surface  Egg surface proteins evolves rapidly to avoid being recognized  Sperm evolution has to keep up, millions of sperm to one egg helps them do that Role reversals  What conditions cause females to compete for mates? o Syngnathids (sea horses and pipefishes) o Males carry developing embryos o Females compete for mates Family sacrifice  Offspring quality can be just as important as quantity  This may explain why male sand gobies eat their developing babies o Paternal care (guarding eggs) is common in gobies o Male sand gobies sometimes eat eggs they're guarding but why? o When density of eggs is high in the nest, makes eat mor eggs  Low oxygen outs all eggs at risk, eliminating some of those potential offspring can help the rest survive rather than them all dying Sex ratios  1:1 ratio of male to females is a typical expectation for Mendelian inheritance of sex chromosomes o It, it's also easy to image that mutations could lead either x or Y sperm to be more successful, skewing the sex ratio o But why are they still 1:1  R.a. Fishers adaptive explanation o Let's say mutation lead to more female births o Makes now have reproductive advantage (easier to find mates o Any mutation that leads to more sons now has the advantage o Presence of more males eventually return selective advantage to mutations for more daughters o Frequency dependent selection/: traits are only favored if they are rare Survival vs. Reproduction  Guppies in Trinidad o Tradeoff between investing in early growth and early reproduction o When small guppies are preferred prey, they prioritize growth before reproduction o When large guppies are preferred prey, they reach sexual maturity sooner o Evolution of flayed reproduction observed in guppies transplanted from high to low predation environment  Semelparity: semelparous species reproduce only one in their life time o Many of these mothers die immediately or soon after giving birth o Natural selection doesn’t favor genes for post reproductive survival o Most species of octopus are examples of this. They live for just a few years so they invest most of their energy into one reproductive event  Iteroparity: iteroparous species have multiple reproductive cycles o Mothers have multiple birth events in a single lifespan o Natural selection favors longer life spans because it allows for more reproduction Menopause in Humans  Life span of human mothers goes far beyond their reproductive age. How might this be adaptive?  Mother hypothesis: prevents women from having their resources divided between older children and babies. Counters increased risk of death during childbirth at old age  Grandmother hypothesis: genetic constraint while increased life span favored by selection. Older women can help raise their grandchildren who have 1/4 of their genes  Or maybe it’s not adaptive at all o Guppies also experience a form of menopause but no grandmother care and presence of predation makes no difference o Maybe just a tradeoff of aging The Origin of Species  We refer to this process of origination of new species as speciation  Species seem to be very easily to identify but there are a couple things that make it more difficult to distinguish different species o Individuals of the same species look very different when there is a lot of INTRAspecific variation  Sexual dimorphism is when different sexes have different traits  Or, there is just a lot of variation o Interspecific variation can cause different species to go unnoticed  Referred to as cryptic species  Defining species o Species concept: a set of criteria used to determine how many species are present in a group of individuals o In the absence of obvious visual clues, other types of evidence like reproductive biology or genetics  Biological species concept o Species consist of populations and organism that can reproduce with one another and do not interbreed with other such populations o Problems with this are asexual reproduction and how some populations are able to interbreed physically but are geologically separated  Phylogenetic Species Concept: species are defined by genetic distinctiveness, specifically by monophyletic groups separated by relatively long branches o Problems: how long is a relatively long branch? What happens when different genes give you different answers/branch lengths? o Usually more evidence than just phylogenetic trees are needed to justify formal description of a new species  Speciation o No matter how you define a sexually reproducing series, reproductive isolation is critical in the process that generates more of them o Reproductive isolation is when two populations either cannot or do not interbreed o This violates the random mating assumption of the hardy Weinberg equilibrium  Allopatric speciation o A population diverges into two species after being physically isolated by some sort of barrier o These barriers come from plate tectonics, island formation, climate, and migration o Let’s say a new river begins to run through the middle of a species' habitat. Genetic drift or natural selection cause different sets of alleles to become fixed on either si


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