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Exam1 Study Guide

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by: Sami Schultz

Exam1 Study Guide PCB4674

Sami Schultz
GPA 3.3

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These notes cover all five chapters that will be included on exam 1. This outline includes detailed notes from the book and class lectures.
Dr. Darin Rokyta
Study Guide
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This 35 page Study Guide was uploaded by Sami Schultz on Tuesday February 2, 2016. The Study Guide belongs to PCB4674 at Florida State University taught by Dr. Darin Rokyta in Spring 2016. Since its upload, it has received 323 views. For similar materials see Evolution in Biology at Florida State University.


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Date Created: 02/02/16
Evolution Ch. 1 01/30/2016 ▯ A case for evolutionary thinking: Understanding HIV  1.1 The Natural History of the HIV/AIDS Epidemic o Worst epidemics in human history:  1. Influenza 1918  2. The Black Death 1347-52  3.New world smallpox 1520 o AIDs is among the worst epidemics in human history  First recognized 1891  HIV infected > 65 million  Every day 13400 newly infected with HIV and 8500 die of AIDS  Infection rates much lower in industrialized countries o HIV contracted when a bodily fluid holding the infection contacts a mucous membrane or bloodstream of an uninfected person o Intro of effective long-term drug therapies for HIV prompted increase in risky sexual behaviors as infection rates for other STIs rose in yr 2000 o What is HIV  Intracellular parasite that can’t reproduce on its own  Uses cells in human immune system to make copies of itself, kills host cell in the process  Extracellular form called virion  Replication initiated by attaching to two surface proteins of host cell (CD4 and a coreceptor)  Virion envelope fuses with host cell membrane and spills virion contents into cell  Contents include diploid genome, reverse transcriptase, integrase, and protease  Flow of genes RNA-> DNA  Difficult to treat b/c HIV uses host cell machinery so any drug that interrupts virus life cycle also interferes with host cell functioning o How does HIV cause AIDS  HIV parasitizes helper T cells, immune system depleted of helper T cells(which respond to invading pathogens)leaving host susceptible to secondary infections  In clinical trial: human HIV patients treated with antiretrovirals+immunosuppressant had higher helper T count than those treated with antiretrovirals alone  T-cell capacity for replication diminishes with each division  1.2 Why does AZT work in the short run, but fail in the long run? o Rationale behind AZT: drugs that block reverse transcriptase should kill retroviruses with minimal side effects  AZT mimics nucleotide to reverse transcriptase picks it up but it lacks the binding site for the next nucleotide o Early tests: AZT worked and stopped loss of marcohphages and T-cells in AIDS patients  Also had serious side effect: stopping DNA synthesis in host cells o Patients stopped responding to treatment after a few years use  Patients cellular physiology changed: long term exposure to AZT could cause natural thymaine kinase production to decrease  Virions become resistant to AZT disruption (~6 mo.) o Difference in resistant vs susceptible virion  Viral strains present late in in treatment were genetically different from those present before treatment  Mutations with AZT resistance occur on active site of reverse transcriptase o no conscious manipulation took place; reverse transcriptase is error prone o change over time in the composition of the viral population is evolution by natural selection o when AZt therapy is stopped, AZT resistant population begins to decrease (back-mutations) o evolution by natural selection  is NOT unidirectional or irreversible  can occur in any population with heritable variation in reproductive success  1.3: Why is HIV fatal o Evolution by natural selection: an automatic process that happens whenever a population shows the necessary heritable variation and reproductive success. Traits conducive to surviving and reproducing spread throughout the population; traits conducive to dying without issue disappear o Short-sighted evolution  Epitopes: short pieces of viral protein displayed on surface of virion or infected cell that help antibodies and killer-T cells recognize HIV  Epitopes mutate; those that better evade the immune system replicate more increasing their population  Evolution of HIV contributes to collapse of immune system  Continuous evolution towards novel epitopes enables viral population to stay ahead of immune response to replicate in high numbers  Viral population in host evolves towards ever more aggressive replication  At least half of all hosts strains of HIV can infect naïve T cells o Correlation between lethality and transmission  Syndey blookbank cohort has a relatively benign strain of HIV  Genome lacks part of gene for viral protein Nef.  Nef helps HIV virions enter host cells  Loss of this function limits damage ot host immune system (b/c lower viral loads)  Second level of selection: those that are god at getting transmitted to new hosts will become more common over time  Poor transmission may be due to reduced ability of Nef- deficient virions to infect new cells  w/ fewer virions in body fluid reduced chance of transmission  1.4 Why are some people resistant to HIV o resistant indivuduals might have unusual forms of coreceptors that thwart HIV entry to cell o resistant genome distribution does not reflect HIV distribution  allele CCR5-delta-32 may have recently been favored by natural selection in European populations  allele could have risen to high frequency by chance as a result of genetic drift o there are also costs to the delta-32 allele such as increased susceptibility to west nile virus  1.5: Where did HIV come from o HIV virus derived from primate’s SIVs o How do researchers reconstruct evolutionary history  Phylogenetic tree shows historical relationships among a group of organisms/viruses  Done by comparing nucleotide sequences o The origin of HIV  HIV-2 Probably transmitted from sooty mangabeys (pets and food) to humans in west Africa  Chimps as food transmitted SIVcpz to humans evolved into HIV-1  Virus jumped from chimps to humans on three separate occasions o HIV diversity and the difficulty of developing a vaccine  Vaccine would need to contain epitopes from all strains of HIV  Likely for transmission of SIV to humans to occur again  Aim for regional vaccine has a higher probability for success ▯ ▯ The Pattern of Evolution  Scientific theories have two components: a statement about an existing pattern and a process that explains that pattern o Theory of special creation  Part one:  Species do not change through time  They were created independently of one another  They were created recently  Part two: separate and independent acts of creation by a designer  Darwin’s evidence against theory of special creation: o Species are not immutable but change through time o Species are not derived independently but from common ancestors o The earth and life are considerably more than 6000 yrs old  2.1: Evidence of change through time o evidence (for descent with modification) from living species  monitoring natural populations microevolution can be directly observed  monitoring the bodies of living organisms shows evidence for macroevolution  direct observation of change through time  soapsberry bugs  feed using long beaks to attack inflated fruit capsules on host plants  before 1925 bugs in FL lived exclusively on native host  gardeners introduced an Asian relative of this plant with flat fruit  bugs living on flat capsuled host had much shorter beaks than the bug living on round capsuled host  short beaked are descended from long- beaked, just evolved when they switched to a new host  alternative explanation: as they grow the bugs develop a beak just long enough to reach the seeds of the fruit they find o refuted by results because the two populations are genetically different  vestigial organs  vestigial structure: useless or rudimentary version of a body part that has an important function in in other, closely allied, species  ex: flightless bird w/ stubby wings; boa w/ remnants of hind limbs; human tailbone and muscles on hair follicles  vestigial traits also occur at molecular level  chromosome 6 has one that disables the production of CMAH, which most mammals make in abundance  evidence: threespine sickleback: small fish  marine have heavy body armor while freshwater have light body armor  when each were mated with each other in a lab offspring were heavily armored; F2 generation consisted of 1.heavily armored 2. Fully plated w/ vestigial pelvic structure 3. Lightly plated with full pelvic structure 4. Lightly armored (suggests control by 2 mendelian genes) o evidence from the fossil record  fossil: trace of organism that lived in the past  fossil record: total worldwide collection of fossils  the fact that fossils exist that are unlike living species today is evidence that life changes over time  three specific observations are evidence of evolution  1. The fact of extinction  list of extinct species directly refutes that unusual forms in the fossil record would eventually be found as living species  creationsists argued that species had died in seried of biblical floods  Darwin and other interpreted extinct species as relatives of living ones  2. Law of succession  general pattern of correspondence btwn fossil and living forms from the same locale  3. Tranitional forms  fossil record should capture evidence of transformations in progress: transitional species with a mix of features  archaeopteryx: crow sized animal with feathers and ability to fly; skeleton was reptilian with teeth and three clawed hands and a boney tail  documents transition from dinosaurs to birds o evidence of descent with modification  2.2 Evidence of common ancestry o intro to tree thinking  Darwin invented phylogenetic trees o Ring Species  Documents one species splitting into two  Ex: Siberian greenish warbler; geographic range forms a ring around Siberian plateau  Individuals recognize each other as the same species and interbreeding occurs everywhere they meet except for where the NE form meets the NW form o Homology: the study of likeness; the same organ in different animals under every variety of form and function  Structural and developmental homology  Underlying design of vertebrate forelimbs is similar even though function and appearance differ  Inherited fundamental design from a common ancestor  Embryo observation  Embryos are similar b/c all vertebrates evolved from the same common ancestor and some developmental stages have remained similar as reptiles, birds, and mammals diversified  Molecular homology  All organisms use the same nucleotide triplets to specify same amino acid w/ few exceptions  Reduces deleterious effects of point mutations/translational errors  A unique genetic code could have been advantageous in preventing spread of disease btwn species so why do all organisms use the same one? It was inherited from a common ancestor  Genetic flaw on chromosome 17 of humans  Causes unequal crossing over by incorrect insertion of CMT1A repeat which results in multiple copies or no copies of PMP-22 gene  Common chimps and bonobos share this repeat; its absent in gorillas orangutans and other examined species  Humans more closely related to chimps and bonobos  Processed pseudogenes: nonfunctional copies of normal genes that originate when processed mRNAs are accidentally reverse transcribed to DNA and inserted at a new location  Readily distinguished because they lack introns and promoters  Estimate age of pseudogene because the older it is the more mutations it will have accumulated  Older processed pseudogenes should be shared by a greater variety of species  Modern concept of homology  Homology underlies use of model organisms in biomedical research and drug testing o Relationships among species o Evidence of common ancestry  2.3: The age of Earth o uniformitarianism: claim that geological processes taking place now operated similarly in the past o the geologic times scale  relative dating: object was to determine rock age relative to other strata based on the following assumptions  younger rocks are deposited on top of older rocks  lava and sedimentary rocks were originally laid down in horizontal position  rocks that intrude into seams in other rocks are younger than their host rocks  boulders, cobbles, or other fragments are older than their host rock  earlier fossil life forms are simpler than more recent forms and more recent forms are more similar to existing forms o radiometric dating: assigns absolute ages  uses unstable isotopes of naturally occurring elements half-life  planet about 4.6 billion yrs old  fossils back 2 billion yrs  2..4: is there necessarily a conflict between evolutionary biology and religion o methodological naturalism and ontological naturalism  methodological naturalism: the only hypothesis researchers propose to account for natural phenomena and the only explanations the accept are ones that involve strictly natural causes  ontological naturalism : the position that the natural world is all there is  methodological assumes nothing else exists but ontological believes this ▯ ▯ Estimating Evolutionary Trees  4.1: The logic of Phylogeny Inference o most closely related taxa should have the most in common o synapomorphies identify monophyletic groups  only certain types of homologous characters are useful in estimating phylogenetic trees  synapomorphy: homologous trait that is shared among certain species and is similar because it was modified in a common ancestor; shared, derived traits  monophyletic group: includes an ancestor and all its descendants  bacteria and mammals use genetic code to put them in the same monophyletic clade  bacteria are identified from eukaryotes by synapomorphies such as cell walls containing peptidoglycan while eukaryotes have a nuclear envelope  all synapomorphies are homologous traits but not all homologous traits are synapomorphies  synapomorphies identify evolutionary branch points  speciation starts when two populations become genetically isolated; once genetic separation occurs the species evolve independently and some homologous traits undergo changes (these changed traits are synapomorphies o cladistics approach  must identify which traits are more ancient and which are more derived  outgroup analysis: the character state in the group of interest is compared to the state in a very close relative that clearly branched off earlier  each brank on tree corresponds to one or more synapomorphies  clustered synapomorphies make a cladogram  synapomorphies identified in cladograms by a bar across the branch and a description of accompanying traits/labels  evolution of tetrapods  identified by evolution of limbs in vertebrates  moist, scaleless sil and exchanging gases across skin link amphibia  amniotic egg distinguished amniota o problems in reconstructing phylogenies  similar traits may have evolved independently in different groups of species  not all similar traits are homologues  convergent evolution: occurs when natural selection favors similar structures as solutions to problems posed by similar environments  octopuses and vertebrates did not inherit sophisticated camera eye from a common ancestor; they individually evolved because both species depend on sight to find food and avoid danger  hippopotamuses and crocodiles have eyes on the tops of their head because they spend a lot of their time submerged in water, not because of a common ancestor  ex: wings of bats and birds, streamline shape of sharks and whales, limbless bodies of snakes and legless lizards  species can even share nucleotide sequences without having a common ancestor  reversals: common in DNA; 25% chance of reversal to the previous state; similar traits are not homologous and aren’t synapomorphies  homoplasy: convergence and reversal; similarities not due to homology  distinguishing homology from homoplasy  most efficient to analyze many traits instead of just one or a few  comparing the two results: development of camera eye in octopuses and vertebrates: assuming common ancestor the tree would undergo six changes while assuming convergent evolution implies only two changes  parsimony: biologists consider convergence most likely hypothesis  homoplasius morphological traits aren’t as similar as they initially appear  octopus eyes: light sensitive cells oriented toward opening while in vertebrates they are in the opposite direction  octopus change the shape of their eyeball to focus while vertebrates change the shape of the lens  developmental pathways and and alleles observed in diff species will be similar if they have a common ancestor  resolving conflicts in data sets: the role of parsimony  minimizes the confusing effects of homoplasy and is most accurate  parsimony favors the simpler explanation  4.2: the phylogeny of whales o choosing characters: morphology and molecules  1. Skeletal and other morphological characteristics  2. DNA sequences and other molecular traits  each path has pros and cons  morphological traits essential when the species only exists as a fossil and is very compelling when homoplasy and homology can be distinguished  slow and painstaking work  molecular characters have a reduced cost and a large number of nucleotide can be analyzed very quickly.  Mathematical models can minimize homoplasy  Helps identify reversals  Homoplasy can be difficult to identify in molecular data o Finding the best tree implied by the data  Parsimony with a single morphological trait  Skeletal character closely relate cetaceans and ungulates  Ungulates two major groups: perissodactyls (horses and rhinos) and the artiodactyls (cows deer pigs camels hippos)  Morphological data identifies artiodactyla as monophyletic  Synapomorphies include skull and dental characteristics and ankle bone(astragalus: unusual pulley shape at both ends)  How close are whales and artiodactyla  If whales are closely related to hippos then a logical evolutionary scenario is assumed  After extinction of dinosaurs mammals made living in shallow water habitats and some, whales, became fully aquatic over time while other remained semi-aquatic  Whale-hippo relationship implies dolphins and porpoises are closely related to completely terrestrial forms  Astralagus suggests hippos and whales are not closely related b/c parsimony. The trait would have been gained just to have been lost again by whales  Whales have no ankles but some fossils whales have had hind limbs  Some features of the pulley shaped astragalus are in the earliest whales suggesting that they are descended from an artiodactyl  Controversial though b/c possible that the bones may have belonged to a different artiodactyl  Parsimony with multiple molecular characters  Over 60 traits analyzed  Computer generates all possible trees then maps each character  Most parsimonious pattern of character change is noted for each character  Best tree implies fewest character changes across all characters  Only 15 of the 60 traits were usable; others were either inherited from the common ancestor and variable yet uninformative  Synapomorphies must group two or more taxa  Determined whales and hippos are closest relatives  Homoplasy evident  Whale hippo hypothesis most parsimonious  Searching among possible trees  When lower than 11 taxa a computer program can evaluate all possible trees (exhaustive search- guarantees optimal tree will be found)  Agreement among search methods strengthens findings o Evaluating the best tree  Using other methods besides parsimony: maximum likelihood and Bayesian inference  Likelihood computes probability that alternative trees are supported by the data  When competing trees arise choose the one with the highest likelihood  Bayesian method asks what the probability of a particular tree being correct is  Provide an objective criterion  Evaluating particular branches: bootstrapping  Bootstrapping: evaluating branches based on parsimonious trees; computer creates new data set from existing one by repeated sampling. New data set used to estimate a phylogeny. The more times a branch occurs in a bootstrapped sample the more confident we can be that the branch actually exists  Under 50% certainty is put in a polytomy (point of uncertainty) o Resolving conflict  More confidence in trees that are estimated with  larger data sets,  characters subject to less homoplasy  inference methods most appropriate to data in question  wait for additional data independent of traits analyzed to date  short or long interspersed elements (SINES/LINES)  whales/hippos: no homoplasy in the dataset  new fossils o take home messages  4.3: using phylogenies to answer questions o classification and nomenclature: is there such a thing as a fish?  Systematics: effort to name and classify species  Linnaean: genus and species according to morphological traits (phenetic approach)  Those based on evolutionary relationships are cladistics approaches; should be tree based; only monophyletic groups named  Paraphyletic groups including some but not all descendants of a common ancestor should not be named  Tree based scheme “fish” would have to include tetrapods o Using molecular clocks: when did humans start wearing clothes  Molecular clock allows us to date events not documented in the fossil record  Mutations in DNA that aren’t expressed in phenotype and therefore aren’t acted upon by natural selection accumulate at a rate equal to the mutation rate  Estimate when two species diverged: document number of different neutral mutations observed in two species multiply by calibration rate  Head lice similar to body lice. Body lice live in clothes so must have diverged around the time humans started wearing clothing  Our species originated 100,000-200,000 yrs ago o Analyzing phylogeny: how did chameleons get from Africa to india  Phylogeography: using phylogenies to help determine why species are found where they are  Evidence shows that chameleons diversified via dispersal to new habitats instead of occurring as the supercontinent broke up  Explains presence on volcanic islands that were never part of supercontinent o Co-speciation: when new species of aphids form, what happens to the bacteria that live inside their cells  Coevolution: when natural selection occurs during interactions such as predation, parasitism, and mutualism  Cospeciation: occurs when a population splits into two groups that become genetically isolated and then begin to diverge genetically  Aphids are parasitized by wasps so they may house bacteria that come from the wasp as opposed to ancestral species ▯ The Cambrian Explosion and Beyond  565 MYA first animals appear in fossil record o jellyfish + sponges found are multicellular but small  543 to 506 MYA is the Cambrian period, when most of todays living animal phyla surfaced  five episodes of extinction  start of Cambrian to present is called Phanerozoic eon  18.1 The nature of the fossil record o how organic remains fossilize  fossil: any trace left by an organism that lived in the past  four general categories of fossils  compression fossils: result when organic material is buried in water or wind borne sediment before it decomposes; the pressure leaves an impression in the material below  casts and molds: originate when remains decay after being buried in sediment.  Molds: unfilled spaces  Casts: form when new material fills the space and hardens into rock  Permineralized fossils: form when structures are buried in sediments and dissolved mineral precipitate in the cells; preserves details of internal structures  Unaltered remains: preserved in environments that discourage loss from weathering, consumption by scavengers, and decomposition by bacteria/fungi  Key features of specimen that fossilization depends on  Durability  Burial  Lack of oxygen  Most fossils found in depositional environments (deltas, beaches, lakeshores) o Strengths and weaknesses of the fossil record  Bias in the fossil record  Geographic: fossils tend to come from low land and marine habitats  Taxonomic: marine organisms dominate fossil record but make up only 10% of extant species  Temporal: earth’s crust is constantly recycled when tectonic plates subduct and mountains erode (ability to sample life forms should decline with time o Life through time: an overview  Time scale: eons, eras, periods, epochs, stages  Phanerozoic eon: paleozoic era, Mesozoic era, and Cenozoic era  18.2: The Cambrian Explosion o The Ediacaran Fauna  Earliest dated at 565MYA and youngest at 544MYA at end of Proterozoic era  Mostly compression and impression fossils  No shells or hard parts  Include sponges, jellyfish, and comb jellies  Asymmetrical or radial symmetry  Difficult to determine if complex bilaterally symmetric animals were present at this time  Evidence supports that bilaterians evolved prior to Cambrian  635-551MYA  apparent embryos found fossilized  trace fossils: remnants of burrows, fecal pellets, tracks  difficult to interpret  bilaterally symmetric animals were small but present pre-cambrian period o The Burgess Shale Fauna  Variety of large complex bilaterally symmetric forms  Arthropods, mollusks, vertebrates, and schinoderms  520-515MYA  mostly impression and compression fossils  little overlap with ediacaran fauna  several chordates found, including jawless invertebrates  had segmented trunk muscles and a notochord  had a problematica phylum that are now being redescribed and more successfully categorized  major morphological innovations  large body size, segmentation, limbs, antennae, shells, external skeletons, notochords o phylogeny and morphology  dipoblasts and tripoblasts  ctendephora cnideria and dipoblastic (have two embryonic tissue types)  tripoblasts have three  present n both tripoblasts and dipoblasts:  ectoderm: cells prodice adult skin and nervous system  endoderm: cells produce gut and associated organs  mesoderm  unique to tripoblasts  develops into gonads, heart, muscle, connective tissue, and blood  tripoblasts  most have one plane of symmetry  dipoblasty and radial symmetry evolved before tripoblasty and bilateral symmetry  protostomes and deuterostomes  gastrulation: mass movement of cells that rearranges embryonic cells after cleavage and defines the ectoderm, endoderm, and mesoderm  protostomes: gastrulation forms mouth first  deuterostomes: gastrulation forms anal region first  lophotrochozoans and ecdysozoans  lineages of protostomes  ecdysozoa are molting animals  lophotrochozoans have a feeding structure called lophophore o was the Cambrian explosion really explosive?  Origin of bilaterians  Analyze differences in hemoglobin amino acid sequences  ~900 MYA  chrodates and echinoderms diverged~1000MYA  protostomes and deuterostomes diverged~1200MYA  discrepancy between estimated time clock and fossil record suggest lineages leading to bilateria diverged over Proterozoic but mostly existed as small larva-like organisms that didn’t show up in the fossil record o what caused the Cambrian explosion  Cambrian explosion filled many ecological niches  Environmental changes that made varying was of life possible  Rising oxygen concentration in sea water (due to photosynthetic algae) key to multicellularity and large size and higher metabolic rate  Larger size prerequisite for evolution of tissues  Higher metabolic rate needed for powered movement  18.3 Macroevolutionary patterns o adaptive radiations: occur when a single or small group of ancestral species rapidly diversify into a large number of descendant species that occupy a wide variety of ecological niches  ecological opportunity as a trigger  occurs when small number of individuals or species is suddenly presented with a wide and abundant array of resources to exploit  EX: finches colonizing islands with few competitors and many resources  Mass extinction events or dispersal and colonization  Morphological innovation as a trigger  Diversification of arthropods: associated with jointed limbs, which allow them to move and find food  Adaptive radiations in land plants  Radiation of terrestrial plants form aquatic ancestors in early Devonian ~400MYA  Evolved waxy cuticle and stomata  Alteration of generation  Cretaceous explosion of flowering plants ~110MYA  Made pollination efficient; flower triggered this radiation o Stasis  Theory of punctuated equilibrium: most morphological change occurs during speciation  Demonstrating stasis  Does change occur in conjunction with speciation events or independently  Is rapid change followed by stasis or continuous change  Necessary that ancestral species survive long enough to co-occur w/ new species in the fossil record: phyletic transformation or anagenesis  Stasis and speciation in bryozoans  Relatively few species meet the requirements for stasis studies  Cheilostome bryozoans show a pattern of stasis punctuated by rapid morphological change  What is the relative frequency of stasis and gradualism  No one process occurs alone  Why does stasis occur  Looking at “living fossils” species that show little/no morphological change over time  Horseshoe crabs: show just as much genetic divergence as other arthropod clades even though far less morphological change occurred  Stasis is not from a lack of genetic variability  Habitat tracking/ dynamic stasis: zigzag evolution; large fluctuations that average to stasis when quantified  18.4: Mass Extinctions o mass extinctions: over 60% of species that were alive went extinct over the course of 1 million yrs o five mass extinction events during the Phanerozoic (responsible for 4% of all extinctions in this period) o background extinctions: occur at normal rates  likelihood of a particular lineage to become extinct is constant and independent of how long the taxa have existed  survivorship curves show the proportion of an original sample that survives for a particular amount of time  almost all produce a straight line: probability of extinction was constant  in marine organisms extinction rates vary with how far larvae disperse: those that disperse survive longer than species whose young develop directly from egg  species with larger geographical ranges survived longer than those with limited ranges o cretaceous-Tertiary: high impact extinction:  Evidence for the impact event (of the K-T extinction  Asteroid evidence  iridium concentration in sediment  shocked quartz  tiny glass particles called microtektites  hit at an angle to splash material NW  crater discovery  killing mechanisms  consequences of ejected material  vaporization of anhydrite and sea water would have contributed to influx of sulfur dioxide to atmosphere creating an acid rain  sulfur dioxide also scatters solar radiation which would have led to global cooling; enhanced by dust-sized carbonate, granitic, and other particles that were ejected  soot deposits suggest wildfires occurred  impact strong enough for mass earthquakes and setting off volcanoes  impact would have made a tsunami in the atlantic ocean  effects on oceans  primary productivity of phytoplankton dramatically reduced  temperature and chemical gradients would have been disrupted  decline of organisms occurred over proceeding 500,000 yrs  extant and selectivity of extinctions  extinctions were not distributed evenly among taxa  wider geographical ranges less susceptible to elimination o recent extinctions: the human meteorite  Polynesian Avifauna  ~2000 species of birds extinct over past two millennia in pacific region as a result of human colonization  human predation along with introduction of mammalian predators brought with the colonizers  habitat destruction: slash and burn agriculture, permanently irrigated fields  is a mass extinction event currently underway  focus on habitat loss due to expanding human population  predicting how habitat destruction will impact extinction rates  multiply number of species found per hectare in diff. environments by rate of habitat loss measured from satellite photos  quantify rate that well-known species are moving from threatened to endangered to extinct status in the lists maintained by conservation groups  estimate the probability that all species currently listed as threatened or endangered will actually go extinct over the next 100- 200 yrs  suggested that extinctions now occurring at 100 to 1000 times the normal rate of extinction  where is the problem most acute  tropical rain forests b/c they’re so rich in species  tropics have been relatively unaffected by humans so they don’t have the resilience to human impact of other areas  more than double the amount of cleared forest is effected due to “edge effects”  ▯ Darwinian Natural Selection  3.1: Artificial Selection: Domestic Animals and Plants o Darwin bred pigeons o Tomato  All species of wild tomato have small fruit (think grape tomato)  Ancestor probably had tiny fruit  Chromosome 2 gene called fw2.2 encodes a protein made during early fruit development  Represses cell division (more protein, smaller fruit)  Changes in promoter alter timing of production and amount made  All wild tomatoes tested have a high production allele  All cultivated tomatoes have low production alleles o Artificial selection can change more than size  3.2: Evolution by natural selection o Darwin’s postulates result in descent with modification  Individuals within populations are variable  The variations among individuals are passed from parents to offspring  In every generation, some individuals are more successful at surviving and reproducing than others  The survival and reproduction of individuals are not randomly they are tied to the variation among individuals. The individuals with the most favorable variations are naturally selected o If differences among individuals in a population can be passed to offspring and is there is differential success in those individuals surviving/reproducing then some traits will be passed on more frequently than others o Characteristics will change slightly with each succeeding generation o Selection happens to individuals but populations are what change o Darwinian fitness: the ability of an individual to survive and reproduce in its environment  Relative nature important in determining fitness  Adaptation: a trait or characteristic that increases its fitness relative to individuals without the trait o Darwin’s mechanism of evolution: Natural Selection  Each of the four postulates can be verified independently  3.3: the evolution of flower color in an experimental snapdragon population o postulate 1: there is variation among individuals  snapdragons varied in flower color  ¾ were white with two spots of yellow on lower lip  ¼ had all yellow flowers o Postulate 2: some of the variation is heritable  12 were SS, 24 Ss, and 12 ss o testing postulate 3: do individuals vary in their success at surviving or reproducing  researchers made sure all plants survived but didn’t ensure all plants reproduced  free living bumblebees pollinated the plants  tracked the number of times a bee visted each flower to see reproduction success by exporting pollen  reproductive success by making seeds was tracked by counting the number of seeds produced by each fruit.  The plants showed considerable variation in their reproductive success o Testing postulate $: is reproduction nonrandom?  Expected that one color would attract more bees than the other  Yellow spots on white flowers thought to be nectar guides: attracted twice as many bees as the yellow flowers  White plants also produced more seeds per fruit o Testing Darwin’s prediction: did the population evolve?  The next generation in this experiment has a higher proportion of white flowers (increased from 75% to 77% of offspring)  3.4: the evolution of beak shape in Galapagos finches o beak morphologies reflect diversity of foods they eat o focus: medium ground finch studied by Grant and Grant on Isla Daphne Major  only one spot on island can pitch a camp  few finches migrate on and off the island  population small enough to be studied exhaustively  primarily seed eaters; beak size correlated with seed size across finch species o testing postulate 1: Is the finch population variable?  All traits investigated on tagged finches are variable o Testing postulate 2: is some of the variation among individuals heritable?  Heritability of a trait: the proportion of the variation observed in a population that is due to variation in genes  Stronger correspondence in beak size between relatives  Issues in estimating heritability  Misidentified paternity  Conspecific nest parasitism  Maternal effects  Shared environments  Ground finches with larger beaks make BMP4 mRNA earlier and in larger quantities than finches with smaller beaks o Testing postulate 3: do individuals vary in their success at surviving or reproducing?  Severe drought in 1977  Killed 84% of finches; assumed died of starvation  Fewer seeds were produced for consumption  Medium ground finches did not attempt to breed  Decline in population simultaneous with decline in seed production  More offspring are produced each generation than survive to breed  Third postulate is universally true o Testing postulate 4: are survival and reproduction nonrandom  Types of seeds varied drastically during drought, not just amount  Seeds typically ranged from small and soft to large and hard  Small soft seeds were consumed first during the drought and left only large hard seeds  Only large birds with deep narrow beaks can crack and eat the large hard seeds  Avg survivor had a deeper beak than avg nonsurvivor  Larger birds are favored in drought conditions while smaller birds are favored in wet years o Testing Darwin’s prediction: did the population evolve  All four postulates true in this finch population therefore predicts a change in composition of population  Chicks that hatched in 1978, year after the drought, had deeper beaks  Small evolutionary changes over short time spans can accumulate into larger changes over longer time spans  3.5: The nature of Natural Selection o natural selection acts on individuals but its consequences occur in populations  selected individuals don’t change, they survived through the selection event o natural selection acts on phenotypes but evolution consists of changes in allele frequencies  evolution is dependent of selection of traits with genetic basis, those that are selected for due to environmental changes wont be passed on to next generation o natural selection is not forward looking  evolution is always a generation behind any changes in the environment o new traits can evolve, even though natural selection acts on existing traits  evolution of new traits possible for two reasons  during reproduction in all species mutations produce new alleles  during reproduction in sexual species meiosis and fertilization recombine existing alleles into new genotypes  mutation, selection, and recombination together produce a new phenotype  preadaptation: a trait that is used in a novel way and is eventually elaborated by selection into a completely new structure; happenstance o natural selection does not lead to perfection  phenotypes evolve that “compromise” between opposing agents of selection  ex: large fish tail that attracts females also slows down escape form predators o natural selection is nonrandom but is not progressive  mutation and recombination are random but natural selection is not  evolution by natural selection is non random ; it increases adaptation to environment  there is no trend toward more advanced, complex forms of life  contemporary tapeworms have evolved to be more simpler than their ancestors (no digestive track) o fitness is not circular  favorable doesn’t necessarily mean favorable; only requirement for natural selection is for certain heritable variants to do better than others o selection acts on individuals, not for the good of the species  if an altruistic allele existed that reduced bearers fitness to increase the fitness of others that allele would quickly disappear  infanticide enhances the fitness of some individuals and does not occur for the good of the species  3.6: The evolution of Darwinism o problems with Darwin’s theory that had to be resolved  Nothing was known about mutation so there was no idea as to how variability was generated in populations  Critics argued that natural selection would stop when variability ran out  1900s showed mutations occur in every generation and every trait  Darwin didn’t know anything about genetics and had no idea how variations are passed on to offspring  Mendel’s experiments were rediscovered to show how variation is heritable  Blending inheritance was the belief at the time that argued favorable mutations would merge into existing traits and be lost  Lamarck’s hypothesis was that species evolve through inheritance of changes wrought in individuals (incorrect)  Ex: if a person were to lift weights to become muscular then their offspring would be more muscular as well  Age of earth was estimated at 15-20 MYO at the time  Kelvin calculated that there was a transition from a hot to cold sun and hot to cold earth that gave a limited window when life on earth was possible, too narrow to allow Darwin’s gradual changes o The modern synthesis  Gradual evolution results from small genetic changes that are acted upon by natural selection  The origin of species and higher taxa, or macroevolution, can be explained in terms of natural selection acting on individuals (microevolution)  Restatement of darwin’s postualtes in terms of the synthesis  As a result of mutation creating new alleles, and segregation and independent assortment shuffling alleles into new combinations, individuals within populations are variable for many traits  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 that survives and reproduce, or who reproduce the most, are those with the alleles and allelic combinations that best adapt them to their environment  Outcome: alleles associated with higher fitness increase in frequency from one generation to the next o This view of life  3.7: The debate over “scientific creationism” and intelligent design creationism o history of the controversy  scopes trial of 1925: scopes violated the butler act prohibiting teaching evolution in schools  butler act stayed until 1967  it was overturned when the supreme court ruled it violated separation of church and state  intelligent design theory: infers the presence of a designer form the perfection of adaptation in contemporary organisms o perfection and complexity in nature  Darwinism predicts that complex structures have evolved through a series of intermediate stages  Ex: eyespots in unicellular organisms that undergo structural changes when they absorb light; similar to more complex eyes’ photoreceptors  The argument from biochemical “design”  If complexity is irreducible then it can’t have functional precursors (cilium) and therefore can’t have been produced by natural selection o Other objections  Evolution by natural selection is unscientific because it is not falsifiable and because it makes no testable predictions  Darwin’s four postulates are independently testable  Because earth was created as little as 6,000-8,000 years ago, there has not been enough time for Darwinian evolution to produce the adaptation and diversity observed in living organisms  Radiometric dating deny this  Earth is actually 4.6 billion years old  Because organisms progress from simpler to more complex forms, evolution violates the second law of thermodynamics  “natural processes tend to move toward a state of greater disorder” – the entropy of an isolated system never decreases  true for only closed systems, which organisms are not  energy is constantly being added to living systems so the second law doesn’t apply to evolution  no one has ever seen a new species formed, so evolution is unproven. Because evolutionists say that speciation is too slow to be directly observed evolution is un-provable and based on faith  we can’t observe atoms directly but there is still evidence to infer they exist o what motivates the controversy  concern is what evolution means to human morality and behavior ▯ Mutation and Genetic Variation  Mutation is the only process that creates completely new alleles o Ultimate source of genetic variation  Selection, drift, and migration act on this newly produced variation  5.1: Where New Alleles Come From o pyrimidines: cytosine and thyamine o purines: adenine and guanine o The nature of mutation  DNA mRNA protein  Each of the 64 codons specified a specific amino acid  Genetic code highly redundant, 20 AA to 64 codons  Allele: versions of the same gene that differ in base sequence  Mutation: any type of change in base sequence of DNA  First mutation characterized on molecular level: change in human gene for hemoglobin that results in sickle-cell disease  Difference in hemoglobin due to a single AA change at position 6 in the protein chain caused by a single base substitution in hemoglobin gene  Mutant allele has ad


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