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Winter Midterm Study Guide

by: Sarah Doberneck

Winter Midterm Study Guide GE 70B

Sarah Doberneck

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This is a study guide with answers to the review questions sent out by the professors as well as detailed notes from the lectures this quarter.
Evolution of Life and the Cosmos
Dr. Friscia
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This 26 page Study Guide was uploaded by Sarah Doberneck on Tuesday February 2, 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 161 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: 02/02/16
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 5 1. Explain the evolution of the human eye. a. G­protein coupled receptors acted as sensors and they slowly evolved into the  complex eyes organisms have today. They were duplicated and modified to act as  receptors (opsins). Formed a bowl so we can better differentiate light coming  from different angles. 2. What are some examples of constraints on adaptation? a. Endothermic/exothermic (SA/V) b. Phylogenetic  3. How do genetic drift and natural selection act on different­sized populations? a. Genetic drift is stronger for small populations due to inbreeding depression b. Natural selection is stronger for larger pops because the gene pool is bigger The geologic and fossil records Tuesday, January 12, 2016 Types of fossils  Any evidence of past life  Includes o Whole body fossils  Mummification, frozen, and bog specimens o Preservation of hard parts and petrifaction o Molds and casts o Trace fossils o Chemical traces  Diagenesis-the physical and chemical processes that lead to fossilization  Taphonomy o The study of how fossils relate to modern species. o Creation of fossils is disrupted by  Decomposition, consumption,  exposure, and weathering  Transportation and burial  Fossilization and exhumation o Lagerstätte- fossil localities with exceptional preservation James Hutton  Father of modern geology  Came ho with the idea that the processes we see today are the same ones that have always been on the earth  Uniformitarianism Determining relative ages  Superposition. Older on bottom, younger on too  Laid down flat  Cross cutting relations, older rocks may be cut by younger rocks  If fragments of one material are included in another, then the included material must be older  Unconformities-gaps in time in the sedimentary record o Occurs when no beds are laid in a time period Index guide fossils  Easily distinguishable  Widespread  Short periods of geologist time  Abundant  Called fossil correlation and bio stratigraphy  What much cause problems with this? o Can't be used for all rocks o Might be caused by migration not time period Geologic time scale  Various eras periods and epochs are defined by assemblages of fossils  But. How did. We put dates on then? o Radioisotope dating o Includes carbon dating  Problem: not. Possible to date all rocks by radioactive isotopes o Can't define the age if Some dates to know  Older eat minerals on earth 4.5 Ga  Oldest rocks  Oldest record of life  Beginning of Phanerozoic/Paleozoic Brief history of early life  Origin of life around 3.5-3.8 BYA, right after the late heavy bombardment ended  Early atmosphere is methane, water, nitrogen, hydrogen, carbon, oxygen, Lots of energy in lightning, volcanoes, and uv rays  Miller-Urey experiment o Filled a chamber with a gas mixture similar to what was thought to be the early atmosphere of the earth, added electric sparks, resulted in complex organic molecules  The RNA world o Probably the first self-replicating molecule o Carries information and can act as an enzyme  Model. For the formation of cells o Needed to be able to collect and enclose the material Eukaryotes  Nucleus  Internal membranes  Mitochondria  Cytoskeleton  Larger  Animals, plants, fungi Prokaryotes  DNA free floating  No organelles  No cytoskeleton  Smaller  Bacteria, archaea Phylogeny terminology  Clade o Ancestor plus all its descendants o Also called monophyletic group  Paraphyletic group o Ancestor plus some or most of its descendants o Reptiles are a paraphyletic group because the name does not include their avian descendants Ancestral vs derived  Ancestral (primitive) character: already present in the evolutionary lineage leading up to the group in question o E.g. Eyes in birds, fins on tuna  Derived character: unique to the group in question o Backbone in vertebrates, nursing young in animals Building a phylogeny  Groups are united by characters that are both shared and derived  The tree that requires the fewest number of changes  Each tree is a hypothesis that can be tested  For just 6 taxa, 945 possible dirt trees can be drawn to show how they evolved  Maximum parsimony-mist likely answers one that equips the fewest number of changes (simplest of several methods for building trees) Homology vs convergence  Birds and invests both fly with their wings, but it's fairly obvious their wings are not homogenous. Their wings are convergent- similar structures with similar functions but evolved independently Old structure, new function  Fossils reveal an evolutionary transition, this time from jaw to ear bones on the phylogeny of vertebrates  Evolution has essentially tinkered with existing parts to create a new function Monotremes are strange, but are they primitive?  The platypus and 4 species of echidna are the only extant species  Egg layers, crude lactation  Almost like transition fossils that never went extinct, but are they primitive?  Characters may be primitive, but an extant species by definition, is not  A species with primitive characters has been evolving just as long as one with derived characters  Different combinations of primitive characters mean monotremes are no more primitive than us Feathered dinosaurs take flight  In the evolutionary transition from dinosaurs to birds  Feathers were present long before flight The molecules of evolution  Darwin was convinced inheritance was real, but had no evidence for a mechanism  Blending inheritance was largely hypothetical, yet widely accepted  Fleming Jenkin did some math to show how blending heritage undermined the theory of natural selection Darwin’s solution  He speculated the idea of pangenesis o Atom sized "gem mules" produces throughout the body by cells o Only carried info about the body parts from which they came  Problems o No solid evidence o Suggested that acquired traits could be passed on o What about innovation/novel traits  August Weismann experimentally erupted Lamarckism o Developed germ plasm theory o Inheritance only occurs via germ cells (gametes, sperm and eggs o Germ cells distinct  Mendelian inheritance o Traits as discrete units o Recessive vs. dominant o Showed traits don't necessarily blend  Mendel’s laws o Law of dominance (when both alleles are present, dominant is expressed recessive is not) o Law of segregation (every diploid individual possess a pair of alleles for a given trait. Each parent passes only one copy to offspring, selected at random) o Law of independent assortment (alleles for different traits are inherited independently. Genes sort randomly and independently during gamete formation. Gametes from one individual may ….. X-linked inheritance  In mammals, sex is determined by X and Y chromosomes  Two X means female  Males have one x and one y  Affected father o Carries one recessive allele o Expresses trait o Passes recessive allele to half his kids  Unaffected mother o Passes dominant allele to all kids  Unaffected father o Carries one dominant allele o Can't express trait o Can't pass recessive allele to kids  Unaffected carrier mother o Carries one recessive allele and one dominant allele o Does not express trait o Passes recessive allele to half of kids, dominant allele to other half  Unaffected father o Carries one dominant allele o Can't express trait o Can't pass recessive allele to kids  Affected mother o Carries two recessive alleles o Expresses trait o Passes recessive allele to all kidskin h o All sons have disease, no daughters have it but are carriers Inheritance of discreet genetic units  Illustrates Mendelssohn laws of inheritance DNA as the stuff of inheritance  How did we go from men Searching for DNA structure in the 1950s  Rosalind Franklin discover end that DNA was a double helix by taking a picture of DNA  Watson and some other old white dudes stole her work and got credit before she did  Double helix is a twisted ladder, with covalent bonds creating a strong back bone  Hydrogen bonds are the rungs of the ladder and are very weak RNA vs DNA  RNA has an extra oxygen molecule  RNA uses uracil in place of thymine  RNA is always single stranded and therefore less stable Base pairing rule: A-T and C-G The central dogma  DNA replication o Each strand of DNA acts as a template to create two new strands o Base pairing rule allows you to make copies without losing info  Transcription from DNA to mRNA o One Sid elf the DNA ladder acts as a template for single strand RNA  Translation of mRNA to protein o Transfer RNA has anticodon at one end, corresponding amino acid at the other end How DNA is stored  Prokaryotes o Single chromosome o Circular, free flowing o Smaller ringlets of DNA called plasmids o Exchange plasmids via horizontal gene transfer (recall the ring of life)  Eukaryotes o Multiple chromosomes o Chromosomes wrap around his tones o Isolated by nucleus o Organelles of prokaryotic origin The hidden genome  Central dogma doesn't explain as much as we thought  We have about 20,000 genes that codes for proteins, and that makes up about 1.2% of the genome  What the other 99% all about? o Not junk o There is a lot of gene regulation as to where and what and when stuff can happen o Gene regulation may be more important than the proteins themselves because it adds to diversity Mutations generate variation  Point mutation o Changing one nucleotide to another  Insertion o Adding in the genome  Deletion o Removing  Gene duplication o Duplicating part so that now there is twice as much of that specific gene in a row  Inversion o Sections get inverted and changes how the gene is read  Chromosome fusion  Genome duplication Codominance  Both alleles are expressed equally o White mom, brown dad cow, calf is spots of white and brown, not just a lighter brown cow Incomplete dominance  Intermediate expression of the two alleles o With link flowers, they come from red and white flowers yet still have the gene for red or for white and can still pass it on Polygenic traits  Multiple genes affect one trait  Ex. Height or skin color Pleiotropy  One gene affects several traits  Ex. Frizzle gene in chickens. One gene give curlers feathers, high metabolism, and low body temp The central dogma says evolution happens primarily at the level of proteins and their genes, gene regulation contradicts this. It's not the proteins that change, it's the way they are expressed Genotype to phenotype  How see phenotype so related to genotypes? It's not simple or easy to do because of polygenic effects, Pleiotropy, and environment Thursday, January 21, 2016 Polygenic-height is influenced by more than one gene  Continuous traits are usually polygenic  Environmental factors often influence continuous traits Real world example of genetics  Diabetes o An inability of cells to absorb glucose due to problems with insulin o Affects .3% of the population o Two types  Insulin dependent (juvenile or type I)  No ability to produce insulin  Produce autosomal recessive with 70% penetrance  Non-insulin dependent (type II or adult)  Lack of sensitivity to insulin  Generic and environmental components  Using type I…  If we assume everyone who is homozygous recessive has the disease, only people with dd can have it. This means that Tony's dad was dd, as were his aunts. Tiny is Dd because he doesn't have the disease. This means his mother either had DD or Dd  What is the probability of each of those two possibilities?  We know that .3% of the population have dd… That is .003 o If q=f(d) (the frequency of the d allele in the population) o .003=q^2….=.55 Hardy Weinberg equilibrium  A statement of how allele frequencies relate to genotype frequencies under certain conditions o F(D)=p=frequency of the dominant allele o F(d)=q= frequency of the recessive allele o P+q=1  Conditions o Random mating o Large populations o No migration o No mutation o No natural selection o If these aren't met, then gene frequencies will change--evolution Breaking HWE: Nonrandom mating  Humans usually mate in groups o We find mates similar to ourselves o 1/3 of all marriages worldwide are between people born less than 10 mi. Apart  Nonrandom mating is due to: o Cultural practices o Imperialism/genocide/rape  Can lead to problems of consanguinity  If you're not mating with people far away and tend to keep all their genes in one community, then at some point you're going to marry someone you're related to  Increased changes of diseases Small populations  Less genetic diversity  More susceptible to random events  Genetic drift: random changes in allele frequency due to the effect of limited genetic sampling with each generation  Starts with some YY, YR, RR… Goes to RR mostly and some YR… Ends with all RR Drunk guy analogy  Alleles frequency-position on platform relative to edges  Time-distance walked  Population size-width of platform  Allele is lost (frequency =0%) o Drunk guy dies  Allele is fixed (frequency =100%) o Drunk guy catches train and goes home Founder affect  Applied to founding populations, it is an unrepresentative sampling of the original population due to chance because of small populations Evidence for genetic drift  Has been demonstrated and quantified in lab experiments  Neutral changes in DNA that are uses to assess evolutionary relationships  Population bottleneck in the elephant seal o Elephant seal numbers were reduce by hunting to less than 25 individuals in the 1890s. There are now more than 30,000 but they show significantly less genetic variation (loss of alleles) relative to mammals with a similar population size o Their population grew faster than the DNA could create mutations  More important in small populations and small populations are a concern for conservation biologists o Drift can result in loss of genetic variation (number of alleles per gene in a population) and can be made worse by inbreeding Selection  Selection favors the fittest in the population, I.e. Those that have the most offspring  Selection can be artificial or natural  This will change the gene frequencies in the population because the phenotype a that selection acts on are based on genotypes Locus- a place on a chromosome (often referred to as a gene) like eye color Allele- a particular variant at a given locus, like brown, hazel, blue As diploid organisms, we have homologous pairs of chromosomes  For a given locus we have 2 alleles (an entire population may have many more than 2) Central dogma explains how DNA (genotype) carries the information for making proteins (phenotype)  Genotypes are inherited. Phenotype star subject to natural selection o Natural selection acts on the proteins (not directly on DNA, but on the expression of DNA) o But it's the change in genotype frequencies over time that defines evolution  Evolution must happen at the level of protein coding genes o Thought that Only about 1% of the entire genome that is important in evolution  However, gene regulation affect how the protein coding genes are used and when they are used which is almost equally as important Two important points: 1 Phylogenetic trees represent the evolution of species 2 They are built using one or more characters from those species, rather than all of them therefore they are a hypothesis to be tested Trees sometimes are made using just fossils, which makes them rely more on morphology  Forelimbs, teeth  Life history traits o Particularly useful for invertebrates, where the adult stage of life is often dramatically different from larval states o Limmaeus and get barnacles were mollusk so because they looked similar... But larval characters were then used to reclassify them as crustaceans Molecular phylogenetic  Overwhelming majority of phylogenetics are now reconstructed using DNA sequence data o Ideally more objective o Lots of available data o Capable of resolving both young and old relationships  Homologous dna o Homologous characters are defined by common descent o Just as important for DNA sequences as it is for morphology o DNA sequences must be different but not too different  Differences are informative. Whole similarities allow alignment of homologous sites  Dna sequence alignment o DNA sequences must vary between species because then there's nothing to compare o Can't differ too much though because then it's useless  Distance matrix o Number of substitutions (DNA or amino acid) between any two taxa o You can get change sin DNA that don't change entire amino acids made by the protein, so by substituting the DNA for the amino acid and comparing the alignment of that instead there will be less changes  Gene trees do not always match species trees o You can map how the gene evolved. But not how the species evolved o The genes move around between individuals of a given species, but only until that population diverges into two species o Notice that some purple dots have no offspring, others have more than one (this is genetic drift and/or selection)  Incomplete lineage shortage o Gene trees don't always match the species trees, results in inaccurate information o How is it fixed?  Use more than one gene, ideally the correct signal will be more prevalent than the one that are wrong o Use math to model how DNA evolves  Use computer programs to detect changes Phylogenomics  Entire genomes can provide results with high confidence  Very computationally intensive  Uses hundreds of thousands of loci because the entire genome is too big  Choosing loci o Quickly evolving genes helps us resolve more recent relationships  Micro satellite loci are used to look at populations because they are so quickly evolving and will stay in the group you're looking at o Slowly evolving genes help us resolve deep relationships  Protein coding genes led to amino acid sequences that allow for cross specie analysis The modern synthesis  A grand unifying theory of evolution  Synthesized evolutionary ideas of: o Biologists (natural. Selection) o Mathematicians (population genetics) o Paleontologists (fossil record)  Evolution is consistent with known genetic mechanisms and the observational evidence of naturalists  Evolution is gradual, small changes accumulate over long periods of time  Natural selection is by far the main mechanism of change, even slight advantages are important when continued across generations. The strength of natural selection in the wild was now considered greater than previously expected  The role of genetic drift is minimal  Must think in terms of populations not individuals. Genetic diversity in natural populations is a key factor  Extrapolation from micro evolution to macro evolution is proposed Neutral theory  Introduced by motoo Kimora 1958 o Contradicted neo Darwinist view of the modern synthesis o Most observed mutation have no effect on fitness o Most DNA is non coding  Protein coding genes are broken up into chunks that are non-coding (introns)  Protein coding exams are often much shorter than the introns that interpret them  Silent mutations rule o Changing the third position protein doesn't see like a big deal because you still get the same amino acid so it doesn't seem like a mutation but it is The nature of mutations  Enzymes repair DNA damaged by oxidation, UV radiation, etc.  They also correct mistakes in the DNA o This is not a perfect process, sometimes mutations aren't repaired and become genetic variants o If it happens during gamete formation, mutations can be passed to offspring Molecular clocks  DNA changing without having an effect in phenotype  Graph looking at how long it's been since two species were similar  Some genes evolve more quickly than others o For example, protein coding genes evolve more quickly in warmer environment Branch length  Nodes represent lineage splits, and tips represent extant taxa  In a cladogram, the length of branches mean nothing  In a phylogram, they represent the amount of evolutionary change (# of DNA substitutions. Indicated by scale bar) Time calibration  Turn a phylogram into a  Fossils are most commonly used to give an absolute age  However, not all species have fossils  Using biogeography, you can look at geologic or climatic events that separated populations which led the, to evolve and become distinct species  Global cooling o Warm water coastal snail communities Breaking hardy Weinberg equilibrium  Selection favors throttles tin the population, I.e. Those that have those offspring  Selection. Can be artificial or natural  This will change the gene friendliest in the population because the phenotype a that selection acts on are based on genotypes Adaptation  The grants have been measuring the finches on the Galápagos Islands for decades  A drought hit the island in 1977, and only large seeds were found  Within that time, there was a change in the average beak sizes o There was a variation in beak size o More individuals were produced than could survive o That variation elated to survival o The variation was heritable Industrial melanin in the peppered moth  Moths come in light or dark shades  In the late 1800s they measured a spread of the dark forms, amount of dark increased  Culturally, this was the industrial revolution meaning a lot of coal was being burned and releasing that pollution in the air o Killed the lighter, greener things on trees and rocks o Soot collected on the trees o No the dark form was much better camouflaged because the trees had soot and lacked miss  Bernard kettle wall tested the pollution hypothesis and found strong support for the impact of moth color on susceptibility to bird predation  In 1958, the uk passes the clean air act, resulting in less pollutants o Looked at the moths again, found there were fewer and fewer of the dark forms as the likins returned  1963 the us passes their own clean air act o Looking at a moth in Michigan similar to the English one, also found an almost exact change in the amount of dark moths that went away while light months increased Malaria  History of the evolution of DDT resistance o Spread a whole bunch of DDT to kill off malaria because they knew it would kill it o After this, the number of people affected with malaria went down by a lot o However, about half a century later, it was back with just as many people affected  By 1970 the mortality rate of mosquitos was a fifth of what it was at first even with ten times the dose  They evolved a resistance to ddt  All 4 premises are met o Mosquitos vary in resistance o They reproduce and more are produced than survive. They are subject to selection in the form of didn't poisoning o Vary in character that affects resistance o Resistant mosquitos live and pass on that trait Clearly, there are limits to the power of selection and structures are produced that are less than ideal  Constraints imposed under phylogenetic history. Evolution builds on what is there. We are descended from a quadrupedal ancestor, so some aspects of our anatomy such as our backs, knees, and feet are adequate but often fail  Lack of appropriate amount of genetic variation  Natural selection can't act on traits that appear post reproductively. The deleterious genes have already been passed onto the next generation  Developmental interactions among organs or structures that necessitate tradeoffs. For example, having larger babies might compromise female pelvic and hip structure Modes of selection  Directional. One extreme phenotype is the most fit  Stabilizing. An intermediate phenotype is the most fit  Diversifying. Two or more phenotype are more got than the intermediates between them Selection can act of multiple traits creating an adaptive landscape Different modes of selection exhibit different departures from hardy Weinberg equilibrium  Directional o More with AA survive , so you get more homozygous and excess dominate  Excess heterozygosity  Excess homozygosity Example of balancing selection: sickle cell hemoglobin  One allele in the beta-hemoglobin locus encodes sickle cell hemoglobin o This carries oxygen led effectively o Red blood cells adopt a sickle shape and break down easily  In the absence of malaria, AA homozygous have the highest fitness o sS homozygous have severe Armenia and usually die before reproducing o AS heterozygous survive  In areas we here malaria is common, heterozygous have the highest fitness o SS homozygous have severe Armenia, die before reproducing o AS heterozygous, have slight anemia and some malaria resistance o AA homozygous have high mortality rates from malaria  S allele has aligned frequency where malaria is common Another example of selection in humans: lactose persistence  Humans normally lose the ability to process lactose as they grow  In populations that domesticated cows early on, there has been selection for a persistence of the lactose producing ability  Genes following the selective gradient here Drift and selection tend to be in opposition of each other  Whichever wins depends on the population size Adaptation  Bacteria example o The broth medium that the bacteria were gown in container a compound called citrate o Normally they can't process citrate in an aerobic environment, but eventually they were able to o A duplication in the gene allowed this to happen Gene duplication is often the tool for adaptation  Evolution is a tinkerer, doesn't make new material but uses what is already there  The gene tree allows us to see these evolution of these changes o Example... Beta defensin are usually used for fighting off bacteria in vertebrates. Eventually, snakes used this in their venom HIX genes  Set up are of body orientation  Where to get arms legs head  Highly conserved, works the same way in the exact same genes across many species Humans have the Same HIX genes compared to flies  Duplicate events through evolution mean we have more than flies do  Limb axes o Axes are determined on the limbs in a similar manner to the axes for the entire body Evolutionary axis  A fish limb develops very differently the a vertebrate limb o Fish are very symmetrical, we are not  Polydactyly o Extra limbs o Happens went the gene for making like a finger or something didn't turn off at the same time  Flippers o Extra bones in their limbs Constraints on evolution. Why are there no mammals a big as dinosaurs?  Mammals are endothermic o Generate heat internal o Benefits  Sustained activity  Active at night  Adaptation to cold environments o Costs  Require lots of food, needs about 10-30 times the food as ectotherms  Not efficient at small body sizes  Ectothermic o Need external sources of heat o Primitive condition o Benefits  Adaptation to not environments  Need little food o Costs  Capable of only short bursts of activity  Limited ability to adapt  Why is endothermic not efficient for small bodies? o Small animals have a hard time retaining heat became they have high surface area to volume ratio o Large animals have a problem getting rid of excess heat because they have a low surface area to volume ratio Phylogenetic constraints  Nearly all mammals have 7 neck vertebrae  The evolutionary history of mammals is the cause of this. The original ancestor had this trait and now it is passed in  It's a constraint... o Pleiotropy-one gene, many effects o Mutations in the number of vertebrae seem to be associated with still births and a higher incidence of cancer  This can make some weird effects... The laryngeal nerve o In mammals, this nerve leaves the skull, wraps around the foes back to innervate the larynx o This makes sense with evolution because based on the anatomy of fish, which we are ancestors of some sort of fish, and as we developed a neck the vein stretched out and went the same route that it was before o Although it could've just gone a few inches to connect, it loops all the way around and goes a couple feet because with the fish it was the most efficient route Convergence: ecological constraint  Marsupial versions of placental mammals  Going back to plate tectonics and Pangea, marsupials were evolved during the time when all the continents were together  When Australia was already separated, placentals began to evolve but the marsupials couldn't evolve with them because they were separated  Whales show convergence on analogous torpedo like body plan Natural selection vs. neutral evolution  Is Kimora's neutral theory compatible with Darwin’s theory of natural selection o Neutral mutations are common o Functional mutations are rare but they do occur  Genetic drift vs. natural selection o Genetic drifts randomly acts upon neutral variation to fix or eliminate alleles relatively slowly (stronger in small populations) o Natural selection is always acting upon functional variation to fix or elimate alleles relatively quickly (stronger in large populations)  They are compatible. The strength of selection and population size determine their relative importance Detecting selection  Synonymous substitution o Does not change anime acid o Silent substitution  Non synonymous substitution o Does change amino acid  Selection for language o Something about changes in the FOXP2 gene seems to have given humans a unique ability to form and use languages o Positive selection at FOXP2 suggests this. People with mutations in this area have severe language disabilities o How this works is still unclear


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