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Study guide for Evolutionary Biology Exam 1

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by: America Seach

Study guide for Evolutionary Biology Exam 1 BIOL

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These are notes from the textbook for exam 1.
Evolutionary Biology
Study Guide
evolution, Biology, Clemson, HIV, mutations, Phylogeny, intelligent design, creationism, Evolutionary Biology, Exam 1
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This 20 page Study Guide was uploaded by America Seach on Thursday January 28, 2016. The Study Guide belongs to BIOL at Clemson University taught by Sears in Spring 2016. Since its upload, it has received 199 views.


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Date Created: 01/28/16
Evolution Notes Chapter 1: A Case of Evolutionary Thinking: Understanding HIV 1.1: The natural history of the HIV epidemic - 1981 is when it was first reported as a rare pneumonia/cancer among gay men - HIV has infected of 65 million people and 30 million have died because of it - The cause of 3.1% of deaths worldwide - Most devastating in Sub-Saharan Africa with 1 in every 20 adults living with HIV, Swaziland has 26% of its adults infected - How it spreads: when a bodily fluid that carries the virus from an infected person comes directly in contact with the mucous membrane or the bloodstream of an uninfected person - Antiviral drugs reduce the risk of mother passing to child by 40%, also effective in gay men - Circumcision reduces the risk by half - Antiviral vaginal gels effective for women - What is HIV? An intracellular parasite incapable of reproducing on its own; it invades specific cells in the human immune system; hijacks the enzymatic machinery, chemical materials, and energy of the host cells to make copies of itself and kills the host cell in the process. - HIV LIFE CYCLE 1. HIV’s extracellular form (VIRION) encounters a host cell, usually a helper T cell 2. HIV’s gp120 surface proteins first bind to CD4, then to a coreceptor (usually CCR5) on the surface of the host cell 3. The virion fuses with the host cell; HIV’s RNA genome and enzymes enter the host’s cytoplasm 4. HIV’s reverse transcriptase enzyme synthesizes HIV DNA from HIV’s RNA template 5. HIV’s integrase enzyme splices HIV’s DNA genome into host cell’s genome 6. HIV’s DNA genome is transcribed into HIV mRNA by the host cell’s RNA polymerase 7. HIV’s mRNA is translated into HIV precursor proteins by host cell’s ribosomes 8. A new generation of virions assembles at the membrane of the host cell 9. New virions bud from the host cell’s membrane 10. HIV’s protease enzyme cleaves precursors into mature viral proteins, allowing the new virions to mature - Notable feature of the HIV’s life cycle is that the virus uses the host cell’s enzymatic machinery, such as its polymerases, ribosomes, tRNA, etc; this makes it difficult to find drugs to interrupt the viral life cycle without destroying the host cell’s enzymatic functions; HARD TO TREAT; Antiviral drugs usually target specific enzymes of the virus such as reverse transcriptase and integrase - How does the immune system react to HIV? Dendritic cells patrol vulnerable tissues (lining of the digestive and reproductive tracts) and when it captures a virus, it travels to the lymph node to show naïve Helper T cells the bits of the virus’s proteins; when the helper T cell’s T-Cell receptor binds to the viral protein, the helper T cell is activated and divides producing EFFECTOR helper T cells to coordinate an immune response; Effector helper T cells releases commands known as CYTOKINES that cause immune cells to join in the fight, inducing B cells to mature into plasma cells that produce antibodies that attach to virions (marking them for elimination); Killer T cells are activated that destroy the infected host cell and macrophages come in and “eat” the destroyed particles; - Most effector helper T cells die, but some remain to become memory T cells that will attack and restart this process if the virus attacks again - How does HIV cause AIDS? HIV’s attack on the CD4 T cells in the gut initiates a vicious cycle that destroys large amounts of helper T cells but also damages other tissues in the gut that provides a barrier between gut bacteria and the bloodstream. The bacteria gets in the blood and triggers high level of immune activation and HIV contributes; Over time, the lymph nodes that make T cells gets worn down and cannot produce T cells and the immune system loses its ability to fight causing AIDS - You can stop the replicating process by using AZT (a drug) to prevent HIV turning into AIDS, but only works temporarily 1.2: Why does HIV therapy using just one drug ultimately fail? - Goal is to inhibit enzymes that are special to the virus and its life cycle - For HIV, potential targets are protease, integrase, and reverse transcriptase - AZT interferes with reverse transcriptase - Reverse transcriptase makes the DNA with building blocks (nucleotides) stolen from the host cell - AZT stops reverse transcriptase; it can fool reverse transcriptase because it looks similar to thymidine, but it lacks a hydroxyl group that is necessary for bonding; this makes it unable to add more nucleotides onto it and blocks the ability to produce a new virion - After using AZT for a few years, patients bodies stopped responding to AZT - Possibly stops working because Patients cellular physiology changes either by producing less phosphorylated AZT or because virions become resistant to AZT - In many patients taking AZT, drug resistant populations of HIV evolve within just SIX MONTHS - What makes HIV resistant to AZT? Thought that the reverse transcriptase enzyme is altered and still picks up the AZT and puts it in the growing DNA strand, but then remove the AZT and can still build their DNA copy- Allows the HIV virions to replicated in the presence of AZT - The changes occurred because reverse transcriptase makes so many mistakes yet it produces so many generations of HIV replication during an infection that multiple variations of REVTRAN are found in every host - This means that every host has a few virions that can add and remove AZT, so they survive while the other variants die out, making it so the AZT resistant virions most prominent - Process of change over time in the composition of the viral population is called EVOLUTION BY NATURAL SELECTION - Occurred so consistently that AZT is no longer used in AIDS therapy - Evolution by natural selection requires two things: - Heritable traits that lead to survival and abundant reproduction spread in populations - Heritable traits that lead to reproductive failure disappear - The categories for drugs in use based on the stage of HIV’s life cycle they are intended to disrupt: - Coreceptor inhibitors: these bar HIV from entering host cells in the first place by preventing them from latching onto the host cell’s CCR5 molecules - Fusion inhibitors: these bar HIV from entering host cells by interfering with HIV’s gp120 or gp41 proteins - Reverse transcriptase inhibitors: some (like AZT) inhibit reverse transcriptase by mimicking the normal building blocks of DNA; others inhibit reverse transcriptase by interfering with the enzyme’s active site - Integrase inhibitors: these block HIV’s integrase from inserting HIV’s DNA into the host genome, preventing the transcription of new viral RNA - Protease inhibitors: these prevent HIV’s protease enzyme from cleaving viral precursor proteins to produce mature components for new virions - Experience has shown that when any antiretroviral drug is used alone, it reacts similarly to AZT in that the host quickly becomes resistant - The simplest way to raise the number of mutations required for resistance is to use two or more drugs at once: the mutation that makes HIV resistant to one drug will make it more susceptible to another drug - By reducing the genetic variation for resistance in populations of virions, cocktails of drugs that target different in HIV’s life cycle limit the evolution of resistant strains; this has dramatically improved patient survival - HAART: three or more drugs that block HIV in two or more different ways are nicknamed highly active antiretroviral therapy (HAART); when patients go off of HAART, the viral loads go back up rapidly - HAART cannot eradicate HIV and by the end of 3 years, the HIV populations in 25% of patients evolved resistance to at least one antiretroviral drug 1.3: Are human populations evolving as a result of the HIV pandemic? - CCR5 is an important coreceptor for HIV - Two individuals that were repeated exposed to HIV remained uninfected; were homozygous for a mutant for of the gene that has a 32-base-pair deletion of the normal DNA sequence; known has the Δ32 allele - Mutant allele fails to appear on the surface of the cell; people who have at least one copy of the Δ32 were less common among the HIV infected European population - 9% of Europeans have the mutant allele, completely absent in Asian or African descent - CD4 has a common allele containing the nucleotide C at the 868 position; frequency of over 15% among Kenyans - CC genotype are less likely to contract HIV than CT genotype - Some scientists have suggested that one reason rates at which individuals are contracting HIV have begun to fall in some of worst-hit regions is that many of the most susceptible individuals are already infected; if the African epidemic continues, the percentage of people who have the resistant genotype will rise and the susceptibility will decline - New strategy for antiretroviral therapy use drugs that bind to CCR5 that will stop HIV from latching onto its coreceptor - Δ32 allele may be favored in Europe because 1. By natural selection or 2. Occurred randomly by genetic drift 1.4: Where did HIV come from? - Louisiana v. Richard J. Schmidt: a doctor was having an affair with his nurse/patient and when she ended things, he injected her with HIV; used evolutionary biologist named David Hillis to test the blood and figure out where the blood originated; and it was proven by showing a diagram of how closely related the blood of the patient and the originally infected blood were - The origin of HIV: o A logical hypothesis is that HIV is derived from one of the SIVs and that the global AIDS epidemic started when this SIV moved from its primate host into humans - There is evidence due to Beatrice Hahn showing that SIV has jumped from great apes to humans at least 3 times - The transfer of HIV-1 happened more than 70 years ago 1.5: Why is HIV lethal? - Strains that are good at getting transmitted will become more common as time goes on and the weaker strains will disappear - Rare strains of HIV-1 exist that kill their host more slowly than common strains; suggest that milder strains are not transferred as easily from one host to another - One possible reason HIV infections are fatal: traits that enhance the new virus’s ability to infect new hosts, such as the maintenance of a moderately high viral load, may also predispose HIV to kill - A second possible reason its fatal: during infection, the viral population evolves—to evade the immune system, replicate more rapidly, and use a different coreceptor - Patients in which the HIV population shows a higher rate of nonadaptive evolution progress more rapidly to AIDS; this is consistent with a model of AIDS in which heightened immune activation offers HIV more opportunities to replicate and is thus among the factors that leads to disease; and in turn suggests a third reason HIV infection is fatal: both the virus and its host have unusual properties - Among the unusual features of HIV as a virus is the ability to make a protein, Vpu, that blocks a host defensive protein tetherin - Among the unusual features of humans as a host is that our TRIM5α protein is relatively ineffective in blocking HIV’s replication, apparently because the protein is adapted to fight an extinct virus that afflicted our ancestors Chapter 2: The Pattern of Evolution - The theory of special creation and the theory of descent with modification make different assertions about species, where they came from, and how they are related, as well as different assertion about the age of the earth. There is evidence that can verify these assertions - Theory of Descent with modifications includes five elements missing from special creation: - Microevolution: a species is not immutable, but change through time; EX: average beak size may change from one generation - Speciation: lineages split and diverge, thereby increasing the number of species; EX: an ancestral species of birds may give rise to two distinct descendent species - Macroevolution: over a long period of time, novel forms of life can derive from earlier forms; EX: tetrapods arose from a lineage of fish - Species are derived not independently, but from common—shared— ancestors; all species are genealogically related - The earth and life are considerably more than 6,000 years old 2.1: Evidence of Microevolution: Change through Time - Evidence from selective breeding: example is from Ted Garland testing mice who have been genetically altered mice that want to run on a wheel - Observations on living organisms provide direct evidence of macroevolution by showing that populations and species change over time - Evidence from direct observation of natural populations: flowers grown from seeds that experienced different environmental conditions had different flowering times; purebreds had shortest flowering, hybrids were next, and the 1997 purebreds that had experienced a drought had the longest flowering time - Evidence from living anatomy (VESTIGAL STRUCTURES): a vestigial structure is a useless or rudimentary version of a body part that has an important function in other, closely allied, species; Darwin argued that vestigial traits are explainable under the theory of descent with modification; EX: the brown kiwi is a flightless bird but has tiny useless wings; the royal python has remnants of hindlimbs; humans have the coccyx which has been reduced to the tailbone - Both the anatomy and genomes of living organisms show evidence of descent with modification in the form of reduced or useless parts - Why microevolution matters: species are not fixed entities; it alters nature and can affect the way humans interact with it; and with us interacting with it, it can also cause humans to evolve 2.2: Evidence of Speciation: New Lineages from Old - Species: populations, or groups of populations, within and among which individuals actually or potentially interbreed and outside of which they do not interbreed - Virtue of this definition, known as the biological species concept, is that we can let the organisms themselves tell us whether they belong to the same species; if individuals from different populations have the opportunity to mate but do not or if they mate but do not produce a healthy, fertile young, then they are different species - Evidence from Lab Experiments: fruit flies showed a mating preference depending on their diets; females and males from starch diets would mate more often than a female starch and a male maltose would; same situation for a male and female on maltose diet - Evidence from Natural Populations: observations on living organisms provide direct evidence of speciation by showing that populations can diverge to the point that their individuals can no longer interbreed; 1. Speciation starts with a single population in which there is variation among individuals; 2. Second stage of speciation involves a population divided into readily distinguishable subpopulations that nonetheless still interbreed; 3. Third stage of speciation features distinct populations with limited interbreeding - Speciation ends with distinct populations whose reproductive isolation is irreversible - Threespine stickleback populations have been found in all four stages making it consistent with the hypothesis of speciation - Ring species: offer compelling evidence that one species can split into two; EX: Siberian greenish warbler; their songs change as you move around the Tibetan plateau, and the sides at the end of the loop cannot interbreed; mate everywhere except in central Siberia where northeastern and northwester do not mate - There is no other evidence than the differing location- no genetic boundaries that keep these two birds from mating - Greenish warblers show that over space and time, a species can gradually divide in two - Speciation matters because it gives insight on how diseases can originate in animals and later develop in humans 2.3: Evidence from Macroevolution: New Forms from Old - Evidence when considering whether new life-forms descend from old: fossils - Fossil record: worldwide collection of fossils - Extinction and Succession: o Georges Cuvier (1801)- published a list of 23 species that were only known based on their fossils; controversy ended after 1812 when he published his work on Irish elk which disproved other scientists thoughts that it was related to a living species o Law of Succession: the general pattern of correspondence between fossil and living forms from the same locale o Extinction and succession are patterns we would predict if present- day species are descended with modifications from ancestors 1. Transitional Forms: - Fossils captured evidence of descent with modification from earlier forms- transmutations in progress - Transitional forms: it is a derived form and represents a lineage that had evolved some, but not all, of the novel traits that transform a species (perhaps from aquatic to terrestrial like the pacific leaping blenny) - A fossil transitional bird: most famous transitional form; Archaeopteryx- a crow sized animal that had modern flight feathers that were adept for gliding, if not powered fight- identifying it as a bird, but it also had a reptile-like skeleton (teeth, three-clawed hands, long bony tail); not a direct line of descent from dinosaurs to birds- had a combination of traits from each, indicating that birds evolved from dinosaurs 2. Transitional Forms Allow Predictive Tests of Evolutionary Hypotheses: - Transitional fossils document the past existence of species displaying mixtures of traits typical of distinct groups of organisms; sometimes transitional forms are predicted before they are found, allowing biologists to test hypotheses about macroevolution - Unlike the flight feathers of modern birds, similicaudipteryx’s feathers are asymmetrical - Theropod feathers match intermediate stages predicted by a model of feather evolution in extant birds- this evidence left little doubt that birds evolved from anything but dinosaurs - A Transitional Turtle: Odontochelys- represents the intermediate step in the transmutation of a typical amniote into a turtle - Why Macroevolution Matters: o It is in our everyday life because we are its product o Fish are our ancestors o Hiccups are a legacy of our macroevolutionary past 2.4: Evidence of Common Ancestry: All Life-Forms Are Related - Homology: the study of likeness o Structural homology: it is extensive similarities among vertebrate skeletons and organs § Underlying design of vertebrate forelimbs were similar although they appear different § Darwin analyzed the anatomy of flowers and discovered that although they appear very different, they are constructed from the same set of foundation components; argued that the only way that these things could be so similar is because they descend from a single lineage - Using Homology to Test the Hypothesis of Common Ancestry o Homologous traits can be used to trace shared traits throughout an species o Can predict relationships between animals based off of what animals have a characteristic they have in common and what they have different; when something different comes into play, that shows the pattern of traits evolving o Molecular Homology: similarities do not need to be to be visible to be similar- chromosomes from chimps are also found in humans; makes it difficult to explain the idea that humans and chimps evolved separately - The Predictive Test of Common Ancestry Using Molecular Homologies: o Processed pseudogenes: a genetic quirk regarding molecular homologies § Exons: small coding bits that make up genes § Introns: noncoding intervening sequences § Retrotransposons: retrovirus-like generic elements that jump from place to place in the genome via transcription to RNA, reverse transcription to DNA, and insertion at a new site; human genome is littered with them § Processed pseudogenes are nonfunctional copies of normal genes that originate when processed mRNAs are accidentally reverse transcribed to DNA by reverse transcriptase, then inserted back into the genome at a new location; they are distinguished from their mother genes because they lack the introns and promoters § The older the processed pseudogene is, the more mutations it will have and that allows us to estimate the age of pseudogenes § The theory of descent with modification from common ancestors makes a testable prediction about the distribution of evolutionary novelties among species: they should form nested sets. That they do is evidence of common ancestry § Humans share the youngest of all six pseudogenes only with the African great apes (chimps and gorillas); and four of intermediate age with primates; share oldest pseudogene with African great apes, the Asian great ape, the old world monkey, and the new world monkey § Molecular homology suggesting a common ancestor among primates § All organisms use the same nucleotide triplets (codons) to specify the same amino acids § Having unique genetic code might offer distinct advantages, but it would rule out having a single common ancestor - The Modern Concept of Homology: o Based off of Darwin’s interpretations o Now defined as similarity due to the inheritance of traits from a common ancestor - Why common ancestry matters? o It is a conceptual foundation for all of biology; you can use a database to known which genes occur in two different organisms and figure out which genes are connected to diseases/mutations in certain organisms 2.5: The Age of the Earth • Uniformitarianism: it is the claim that geological processes taking place now worked similarly in the past; direct challenge of catastrophism • Used the rate of rock formation to estimate the time required to produce such rock • The atlantic formed when Pangaea split apart, and it is not done widening- use the time it takes every year to predict the time it took for the atlantic to reach its current width • The Geologic Time Scale: putting rocks and fossils together in order from oldest to youngest to determine what existed when • Radiometric dating: gives absolute ages instead of relative ages (geologic time scale); uses unstable isotopes of naturally occurring elements and measures the rate at which it decays by half (half-life); serve as natural clocks • Several independent lines of evidence indicate that Earth is billions of years old—old enough for the diversity of life to have arisen by descent with modification from a common ancestor • Why does the age of Earth matter? It shows how long descent with modification takes, and the earth took billions of years to make so this supports the idea Chapter 3: Evolution by Natural Selection • Darwin and Wallace combined discovered the ideas of natural selection 3.1: Artificial selection: Domestic Animals and Plants • Darwin studied evolution by domestication, meaning that he took steps such as modifying his “livestock” to produce optimum results - to increase the frequency of desirable traits in their stocks, plant and animal breeders employ artificial selection - consider tomatoes when discussing evolution under domestication: wild tomatoes are much smaller (1 cm across) while domesticated tomatoes are much larger (15 cm or more across); wild tomatoes have higher production of allele fw2.2 that suppresses growth, and larger tomatoes produce lower amounts of fw2.2- farmers used the seeds from the larger tomatoes year after year producing larger and larger tomatoes o fas gene was found that controls the number of compartments in a fully grown tomato o vegetables that look extremely different came from the same wild cabbage o traits that are favorable to humans may not be favorable in nature 3.2: Evolution by Natural Selection - Darwin and Wallace realized that process similar to artificial selection happens automatically in nature - Natural selection: happens automatically in nature; described by Darwin’s Postulates: - The individuals within a population differ from one another - the differences are, at least in part, passed from parents to offspring - some individuals are more successful at surviving and reproducing than others - the successful individuals are not merely lucky, instead they succeed because the variant traits they have inherited and will pass to their offspring - if all four postulates hold, then each generation of a population changes - natural selection is a process that results in descent with modification, or evolution - the field mice example shows that with varying coat color, the darker mice stand out against the sand and therefore get eaten by the herons. Since there are less dark mice to reproduce with, the mice offspring become lighter and lighter each generation - characteristics of the population change slightly with each succeeding generation, known as Darwinian evolution - there is no conscious intent or goal with natural selection- it occurs no matter what and it is just a coincidence that specific traits do better - Darwinian fitness: an individual’s ability to survive and reproduce; do not have to be physically fit; - adaptation: a trait that increases an organism’s fitness relative to individuals lacking it - each postulate can be verified independently so the theory is testable 3.3: The Evolution of Flower Color in an Experimental Snapdragon Population - testing Darwin’s postulates: Can natural selection of bumble bees cause flower color of snapdragons to evolve? o postulate one: individuals differ from one another- snapdragons varied in flower color; ¾ of the flowers were almost pure white with yellow spots on the lower lip and ¼ were all yellow o postulate two: the variation is inherited- the difference in color was based off of a plant’s genotype; SS and Ss are white, ss are yellow o testing postulate three: Do individuals vary in their success at surviving or reproducing? the researchers counted the number of seeds produced by each fruit; consistent with darwin’s third postulate- there were variations in reproductive success o Testing postulate four: Is reproduction nonrandom? at both pollen export and seed production, white flowers beat yellow o Testing Darwin’s Prediction: did the population evolve? Since white plants had higher reproductive success than yellow, and since flower color is determined by genes, the next generation of snapdragons should have had a higher proportion of white flower; white flower population changed from 75% to 77% after one generation o The theory of evolution by natural selection is testable. when researchers set up a plant population in which postulates 1 and 2 were true, they found that 3 and 4 were also true-- as was Darwin’s prediction that the population would evolve as a result 3.4: The Evolution of Beak shape in Galapagos Finches - there are 14 total descendants from dome-nested finches from 2-3 million years ago; close examination of the evolutionary tree reveals that all of the species are closely related - the beaks vary depending on what they eat - testing the theory of evolution by natural selection based on ground finches on Isla Daphne Major; in the average year, there’s a population of 1,200 finches; birds with smaller beaks eat smaller seeds o testing postulate 1: Is the finch population variable? All traits that were studied showed variability- wing length, tail length, beak width, beak depth, and beak length; Some have beaks that are only half as deep as those of other individuals o Testing postulate 2: Is some of the variation among individuals heritable? the heritability of beak depth § heritability of a trait is defined as the fraction of the variation in a population that is due to differences in genes; can be between 0 and 1 § parents with deep beaks tend to have chicks with deep beaks • in finches, the beak depths parents and offspring are similar; this suggests that some alleles tend to produce shallow beaks while other alleles tend to produce deeper beaks • Bmp4 expression is correlated to beak size; more Bmp4, the deeper the beak • Testing Postulate 3: Do individuals vary in their success at surviving and reproducing? o 89% of the geospiza conirostris individuals die before they can breed; o typical for more offspring are produced than the number that live long enough to breed o some individuals that survive to breed do better at mating and making offspring than others o Darwin’s third postulate is universally true o Testing postulate 4: Are survival and reproduction nonrandom? § as the drought progressed, the seeds available for the finches changed- the hard seeds became a key food item, but only large finches with deep beaks could crack/eat them; this shows that finches with larger, deeper beaks during the drought had an advantage in feeding and it allowed them to survive § in wet years, small birds with shallow beaks survived because larger seeds were not as readily available as small seeds § natural selection is dynamic § Testing Darwin’s Predictions: did the population evolve? • because of the drought, the finch population evolved; selection occurs within generations and evolution occurs between generations 3.5: The Nature of Natural Selection - The theory of evolution by natural selection is difficult to understand because it is a statistical process and statistical thinking does not come naturally to most people - Natural selection acts on individuals, but its consequences occur in populations - Natural selection acts on phenotypes, but evolution consists of changes in allele frequencies o no matter what, the finches with the bigger beaks would have survived at higher rates during the drought o only when survivors of selection pass their successful phenotypes to their offspring, does natural selection cause populations to change from one generation to the next - Natural selection is not forward looking o cannot adapt in advance to future conditions and can’t anticipate environmental changes - Although selection acts on existing traits, new traits can evolve o differences in survival or reproduction occur only among variants that already exist o persistent natural selection can lead to the evolution of new functions for existing behaviors, structures, or genes o exaptation: a trait that is used in a novel way; represents happenstance; enhances an individual’s fitness fortuitously, not because natural selection has foresight o secondary adaptations: additional modifications that arise during the process of elaborating a new structure because of an exaptation trait - Natural selection does not lead to perfection o “No guy is perfect” o evolution does not result in organisms that are perfect o natural selection occurs among extant variants and cannot optimize all traits - Natural selection is nonrandom, but it is not progressive o there is no such thing as a higher or lower plant or animal - Fitness is not circular o “survival of the fittest” is misleading - Selection acts on individuals, not the good of the species o individuals do not do things for the good of their species. they behave in a way that maximizes their genetic contribution to future generations 3.6: The Evolution of Evolutionary Biology - Darwin’s original theory had three serious problems: - Variation: darwin had no idea what mutations were so he didn’t know how variability was generated; Thomas Hunt Morgan experimented with fruit flies and began to explain the continuous and universal nature of mutation - Inheritance: Darwin knew nothing about genetics and therefore did not understand how variations were passed to offspring; It was Mendel who confirmed Darwin’s second postulate through Mendel’s laws of segregation and independent assortment - blending inheritance: favorable variants would merge into existing traits and be lost; no matter how advantageous a trait may be, it will be diluted; does not apply to every trait, just phenotypes (not genotypes) - offspring do not inherit phenotypic changes acquired by their parents - Time: the exact age of the earth was not known, just assumed based on different scientists’ work - The Modern Synthesis: o integrating Darwin’s postulates with the new discoveries about genetics to create a modern theory of evolution o resolved decades of controversy over the validity of evolution by natural selection o Darwin’s postulates have been restated: - Individuals may vary as a result of mutation creating new alleles, and segregation and independent assortment shuffling alleles into new combinations - Individuals pass their alleles on to their offspring intact - in every generation, some individuals are more successful at surviving and reproducing than others - the individuals most successful at surviving and reproducing are those with alleles and allelic combinations that best adapt them to their environment 3.7: Intelligent Design Creationism - scientific controversy over the fact of evolution ended in the late 1800s when there was an overwhelming amount of evidence supporting it - the theory of special creation was rejected over a century ago, but creationists now want it taught in public schools - History of the Controversy in the United States o The Scopes Trial: John T. Scopes was a biology teacher who gave his students a reading about Darwinian evolution and it violated the Butler Act (which prohibits teaching of evolution in public school); he was convicted and fined $100; Butler Act was struck down and any other laws prohibiting teaching evolution in public schools in 1968 - Perfection and Complexity in Nature: o The argument from design contends that adaptations--- traits that increase the fitness of individuals that possess them--- must result from the actions of conscious entity o Natural selection produces the appearance of design without a designer o Traits evolve in small increments, but doesn’t always increase in fitness with each step o An example are eyes- the parts don’t really seem like they would work individually, but the eyes of lampreys, hagfish, sea squirts, and lancelets do not have full use of all aspects of the eye, but still have the ability to sense light - The Argument from Biochemical Design o Intelligent design creationism is a modern version of the argument from design o Behe was a creationist that believed that molecular machines inside cells are irreducibly complex (that if someone removed one part, the system would not be effective) and could not have been built by natural selection § He argued that cilia fit this idea of Design and it was disproved over 10 years later - The Eurkaryotic Cilium is not irreducibly complex - Irreducibly complex systems can evolve by natural selection o Like the classical argument from design, the claims of intelligent design creationalism are demonstrably wrong o The capacity to perform simple logical functions evolved first and complex functions evolved later o Enzymes that function outside of the eye are similar or identical to evolved crystallins of the eye - Other objections: additional arguments used by creationists 1. Evolution by natural selection is unscientific because it is not falsifiable and because it makes no testable predictions o Each of Darwin’s postulates is independently testable 2. Because organisms progress from simpler to more complex forms, evolution violates the second law of thermodynamics o The second law focuses on entropy (measures the state of disorder in a system) and says that an isolated system can’t decrease o This is only used for closed ---isolated--- systems, and organisms live in an open system 3. No one has ever seen a new species formed, so evolution is unproven. And because evolutionist say that speciation is too slow to be directly observed, evolution is unprovable and thus based on faith o We cannot observe atoms directly, but we know they exist o Speciation is slow but that doesn’t mean it can’t be studied Chapter 4: Estimating Evolutionary Trees - tree diagrams are used to summarize evolutionary relationships 4.1: How to Read an Evolutionary Tree - an evolutionary tree or phylogenic tree/phylogeny is a diagram showing the history of divergence and evolutionary change leading from a single ancestral lineage to a suite of descendants - How to read time on an evolutionary tree o The root of the tree is where the common ancestor can be found o Lines extending from the root trace the divergence, and they grow over time o Node: a branching point; where it splits into separate groups o Transitions: evolutionary modifications - Phylogenies are hypotheses about the history of descent with modification from a common ancestor that produce a set of species or other taxa; time flows along a phylogeny from the root toward the branch tips - How to read relationships on an evolutionary tree: o Evolutionary relationships: the time elapsed since they last shared common ancestors o Sister species: species sharing a more recent common ancestor with each other than either shares with any other species o Lineages that share more recent common ancestors are considered more closely related - Evolutionary trees do not show everything: o Evidence of the evolutionary history can be missing in all sorts of amounts from trees o A phylogeny speaks only about relationships among taxa that are included in the tree and gives no insight on the taxa that aren’t included - Evolutionary trees can be drawn in various styles: o Evolutionary relationships are depicted solely by the order of branching in a phylogeny - Evolutionary trees are hypotheses: o The trees never reveal the whole truth 4.2: The Logic of Inferring Evolutionary Trees: - Phylogeny inference in an ideal case: o Derived characters: evolutionary novelties that are unique to a species and shared within that species o In an ideal case, we can infer that the evolutionary history of a set of species from their nested sets of shared evolutionary innovations o Can use nested sets of shared derive characters to reconstruct the history of diversification- so to make inferences about the phylogeny - Key concepts in phylogeny inference o Apomorphy: a novelty, derived character o Plesiomorphy: ancestral character; preexisting o Synapomorphy: shared derived character o Monophyletic group: also known as a clade; consists of an ancestor and ALL of its descendants; identified by shared derived traits (synapomorphies) o Paraphyletic group: consists of an ancestor and some of the descendants o Polyphyletic group: a group that contains some of the ancestor’s descendant but does not include the ancestor o Polytomy: a three-way (or more) lineage split at a branching point; uncertainty about order of branching in a phylogeny is indicated by these - Phylogeny inference in non-ideal cases: o Do not know characteristics of the common ancestor that the species of interest is derived from o Similar evolutionary novelties sometimes evolve independently in different lineages o Evolutionary novelties are sometimes lost after they evolve o Outgroup analysis: including in our historical reconstruction one or more additional species that are relatives of the ingroup § Ingroup: the species with the relationship we wish to infer about § Outgroup must be less closely related to the ingroup than the members of the ingroup are related to each other o Parsimony Analysis: § Parsimony: choosing the hypothesis that requires fewest evolutionary changes in the character of interest § Uninformative character: the characters that do not give insight into the analysis § Parsimony analysis allows us to make inferences about questions that might otherwise be unanswerable § Most real examples do not work like our ideal case; different characters often suggest different evolutionary relationships. In such circumstances, we consider all possible evolutionary trees as viable hypotheses and compare them using several criteria- one being parsimony (minimum amount of implications towards the tree) o The number of possible trees: it increases with the number of species in the ingroup - Convergence and Reversal: o Convergent evolution: when similar derived characters appear independently in different lineages o Reversal: the loss of derived traits in a lineage, returning to ancestral conditions o Homoplasy: similarity in character states due to convergence and reversal; independent appearance of a character’s state in more than one place on a phylogeny o Homology is similarity due to common ancestry- synapomorphies are a particular category of homologous traits that are evolutionary novelties to the lineage being studied 4.3: Molecular Phylogeny Inference and the Origin of Whales: - what is a cetacean? o A monophyletic group connected based off of the bones of the skull (making them synapomorphies) o Early cetaceans did not have flippers, were not legless, and did not have dorsal fins; modern cetaceans derived from terrestrial ancestors - Morphological Evidence on the origin of the Cetacea: o William Flowers- thought that cetaceans may be related to ugulates (hoofed mammals) based off of their internal organs § Pigs may be cetaceans’ closest relative placing them in the artiodactyls (even-toed hoofed animals) o The most prominent of the synapomorphies that identify artiodactyls as a monophyletic groups the ankle bone- astragalus - Molecular evidence of evolutionary relationships: o We can infer evolutionary trees using molecular characters, such as nucleotide or amino acid sequences in addition to morphological characters o Aligning sequences: the first step in reconstructing evolutionary history using sequencing data is to align the sequences; we then compare alternative phylogenetic hypotheses using criteria such as parsimony - Evaluating alternative phylogenies with parsimony: o Treat each site in sequence as an independent character and look for sequences that are unique to only a few of the taxa in question o Choose the tree that requires the fewest amounts of substitutions (parsimonious) - Evaluating alternative phylogenies with likelihood: o Calculating the probability of evolving the particular set of sequences we have found in our data o Likelihood: the probability of the data given a tree, its branch lengths, and a model of evolution o Using maximum likelihood as a criterion for comparing phylogenies, we prefer the tree with the highest probability of producing our data - Searching for the best of all possible trees: o Must first consider that all options are possible and the only way to find the best is to look at each one o The number of possible trees is usually so vast that we cannot come close to evaluating them so instead we use computers to find the best hypothesis o Branch and bound: eliminates groups of trees from consideration upon discovering that all their members are worse than the best tree found so far o Heuristic searches: looks for trees superior to the current leader by rearranging the leader in various ways and evaluating the results; the search may have multiple different starting points so it doesn’t get stuck on one peak o Bootstrapping: the generation of artificial data sets by random sampling, with replacement, from actual data set; analyzing the artificial data sets gives an idea of how much the results might change if the study were replicated many times - Bayesian Phylogeny inference: o Using maximum likelihood- the calculated probability of each possible tree is P(data|tree) o Posterior probability [P(tree|data)]: the probability of the tree given the data o Prior probability [P(tree)]: the probability we assigned to the tree before taking the data into account o P(data): prior probability of the data o Easy to interpret results from this type of inference o Clade credibility: the sum of the posterior probabilities of the trees for each clade - Toward a resolution on whales: o Presence or absence of SINEs and LINEs that insert themselves into new locations in the genome--- the presence or absence of a particular sine or line at a homologous location in the genome of two different species can be used to make a phylogeny inference o Some molecular characters come close to presenting ideal cases for phylogeny inference o By using different kinds of evidence based on the evolutionary relationships in question, everything can be cross-checked to determine the correct results o Evidence suggests that ancestors of whales and hippos may have descended form the same semiaquatic ancestor o In the case of whales and their kin, morphological characters show considerable homoplasy 4.4: Using Phylogenies to Answer Questions: - Can tumor cells move from patient to patient? o CTVT is a cancer that grows on dog genitalia; testing where it came from and how its transferred o The results show that the tumors are all more closely related to each other than an is to the dog its growing on o Tumor cells move from dog to dog - When did humans start wearing clothes? o Molecular clock: analyzing molecular traits that change at a steady rate to answer questions about timing o Neutral changes evolve by a random process called genetic drift o Researchers used human body lice to determine when humans started wearing clothes because head lice and body lice are different § Body lice could have only come into existence after humans started wearing clothes because they live in clothing § Compared chimp lice to human lice to find when they diverged § Came up with 107,000 years ago- origin of body lice - How did the Seychelles chameleon cross the Indian Ocean? o Biogeography: where an organism lives and how it got there o Phylogeography: using phylogenies to answer how certain species got distributed geographically o Two possibilities of how the chameleon got to the islands: 1. Vicariance Hypothesis: Did not move because the Seychelles were once part of Gondwana and when it broke up, it stayed on the island 2. Dispersal Hypothesis: It floated on a raft to the Seychelles o Chameleon’s closest relative are African and its last common ancestor lived 40 million years ago o Confirmed that these chameleons rode a raft to the Seychelles


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