Evolution Exam 1 Study Guide
Evolution Exam 1 Study Guide BIOL 3303
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This 112 page Study Guide was uploaded by Madeline Abuelafiya on Wednesday February 17, 2016. The Study Guide belongs to BIOL 3303 at Southern Methodist University taught by Dr. John Wise in Winter 2016. Since its upload, it has received 125 views. For similar materials see Evolution in Biology at Southern Methodist University.
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Chapter 2 Biology: from natural philosophy to Darwin Darwin’s insights form the foundation of evolutionary theory • Explains how patterns of diversity came to be • Combined his ideas with work of many others Early naturalists classified life’s diversity Carl Linnaeus (1707-78): Father of modern taxonomy Some recognized record of historical change Nicolas Steno (1638-86): Father of geology and stratigraphy Early ideas about evolution • Earth formed according to laws of physics and chemistry – Older than previously thought • Life emerged as distinct types – Transformed when environment changed Georges Buffon (1707-88) Paleontology provided evidence that life changed • Georges Cuvier (1769-1832) – Fossils resemble but are not exactly the same as modern species – Many past species are extinct – In 1801 Cuvier published a list of 23 species that no longer existed Cuvier‘s Fossil Evidence of Extinction • The Irish Elk • Hard to overlook... http://www.prehistoric- wildlife.com/species/m/megaloceros.html Megaloceros giganteus Geologists recognized that change was gradual • James Hutton – Observable processes produce small changes that accumulate over time – The earth must be very, very old • far older than the 6000 years J(1726-1797) assigned by theologians from biblical inference. • William Smith – Different rock layers contain distinct fossils William Smith (1769-1839) Smith created first geological map 5 Geologists named rock formations from different periods Sedimentary formations often identified by types of fossils they contain Evolution as striving • Life driven from simple to complex – thought that he saw several lines of descent in collected fossils and current species – Each was a chronological series of older to younger fossils leading tJean-Baptiste Lamarck modern species (1744-1829) • Adaptation occurs through inheritance of acquired changes – False Charles Darwin (1809-1882) • Medical school in Edinburgh – Dropped out Preferred to study nature • Trained to become clergyman at Cambridge • Invited to serve as unofficial naturalist for HMS Beagle in 1831 Voyage of the Beagle • Collected many fossils and living organisms • Studied geology while reading Principles of Geology by Lyell – Uniformitarianism: observable natural processes responsible for events in the past – Saw seashells on a mountain top in South America – Witnessed an earthquake that raised the ground significantly Observations convinced Darwin that life evolved After decades of waiting Prompted to go public • Letter from Alfred Russel Wallace proposed similar evolutionary ideas – Common ancestry – Natural selection • Compromise publishing arrangement set up by Geologist Lyell • Letters from Darwin and Wallace presented at Alfred Russel Wallace Linnean Society in 1858 (1823-1813) • The Society members were “underwhelmed” Darwin’s book published in 1859 • On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life Evolution by natural selection (1) Species are related by descent with modification from a common ancestor (2) Species change through time (3) Changes occur through natural selection 460 pages of “one long argument” Common descent makes sense of puzzling patterns in nature Homologous trait: similar because of inheritance from a common ancestor Common descent makes sense of puzzling patterns in nature Fish vascular anatomy for gills adapted in development for lungs of reptiles/mammals Evolution isn’t intelligent – it is imperfect Recurrent laryngeal nerve – One of the cranial nerves – Goes from the brain through a tube near the heart to the larynx. • Direct route in fish. • Detour of ~ 1-2 feet in humans. • 10 to 15 feet of extra nerve in giraffes. Why? Because evolution and natural selection operates in the short term, with each step taking place as a modification of what is already present. The giraffe is cobbled together from what came before. William Clift's Law of Succession Fossil and modern organisms are related in each area • Important because it connects life forms from one time to another in the same place (required by Theory of Evolution). Huge effect on Darwin in South America • Darwin: Armadillos of Argentina (top, modern pygmy armadillos and fossil nd glyptodont (2 from top) are related. • Richard Owen: extinct Australian mammal Diprotodon (bottom) related to wombat marsupial (2 ndfrom bottom). Reproductive Potential - In every population studied, more offspring are produced than survive to breed. Also known as biotic potential or fecundity. The number of progeny an organism or pair can produce under optimal conditions assuming no deaths in the offspring. In every population looked at, some individuals are more successful at mating and producing offspring than others. In a steady state population (no growth and no decline) an average of 1 offspring per breeding survivor is produced. Postulate that Individuals vary in survival and reproduction is universally true. 11 Natural selection: Darwin’s mechanism of change Overall effect of Natural Selection: On average, surviving individuals / populations will have higher fitness than those that do not survive Leads to Adaptations: traits that have evolved by natural selection Darwin’s theory remains the best explanation for the diversity of life • Natural selection and sexual selection are powerful forces in natural populations • Darwin’s theory has also been expanded – Genetic drift: random changes to the gene pool resulting from chance events – Sexual selection – Kin selection – Group selection (?) Chapter 5 Raw material: heritable variation among individuals Chromosomes come in homologous pairs Ploidy can vary Ploidy: Number of copies of unique chromosomes in a cell Adder’s tongue – 1260 chromosomes Ribosomes translate mRNA into protein Gene expression can be regulated in a number of ways Regulation of gene expression is flexible Non-coding regions make up most of the genome • Non-coding regions include: – RNA genes – Pseudogenes – Mobile genetic elements microRNA can affect phenotypes • Small RNAs that complement mRNAs and enhance or silence expression • Mutants in microRNAs confuse the identity of the flower parts Variation in genome size and complexity Most variation in size due to differences in mobile genetic elements Key Concepts • Most proteins function in four ways: – Enzymes – Cell-cell signaling – Receptors – Structural elements • Mutations are the raw material for evolution • In diploid organisms, deleterious mutations may be masked by a functional gene copy Types of mutation Gene duplication / Unequal Crossing Over Occurs during meiosis when homologous chromosomes line up incorrectly. • Due to repetitive DNA sequences, crossing over can occur in non-homologous (different) locations. – a shortened chromosome (missing a gene or gene segment) – a lengthened chromosome that has a duplicated gene The duplicated gene is free to accumulate mutations, because the copy is supplying the function. 12 Gene Duplication in the Globin Family • In 1st trimester, embryo uses 2 zeta and 2 epsilon globins. – G-gamma and A-gamma then pair with alpha-1 and alpha-2. – Finally adults have two beta-globin proteins paired with alpha-1 and alpha-2 per hemoglobin. • These are functionally distinct proteins – fetal hemoglobins can take oxygen from the mother's adult hemoglobin. 13 Gene Duplication in the Globin Family • Globin family of proteins is thought to have arisen by gene duplication. • Supported by the remarkable similarities in length and position of introns and exons ---------nearly identical------------! yellow is untranslated, green is translated (exon) and white are introns (untranslated). Numbers in the boxes are nucleotides; above the boxes numbers represent amino acid residues. 14 7 Different types of mutation can alter the phenotype Examples of point mutations A. Albinism B. Polydactyly C. Cephalopolysyndactyly E. Fibrodysplasia ossificans progressiva F. progeria 8 Sickle cell anemia – the first mutation characterizedby molecular genetics 1949 – Linus Pauling reports that people suffering from sickle cell anemia have an altered hemoglobin. Oxygen carrier of mammalian blood. 1953 – Watson and Crick publish paper on double change in DNA coding for beta globin (a helical structure of DNA mutation) changes the protein structure958 – Vernon Ingram which changes the cellular shape. shows that sickle cell hemoglobin has an Malaria: amino acid substitution 1.3 to 3 million deaths per year at position 14 of the 1 death per 30 seconds beta chain. mosquito borneciparum parasite – 17 Most Mutations are Deleterious • Fitness declines if mutations are allowed to accumulate and no natural selection is operating to remove the "bad" mutations from the population. • Survival to maturity was measured in normally selected (most but not all reproduce, "control") and non-selected (all allowed to reproduce). C. elegans data – normally selected and not selected • Selection removes deleterious mutations from population; higher fitness results. 18 9 Most Mutations are Deleterious Copies made: 1 10 20 50 75 100 • Data from roundworm, fruit fly, bacteria, yeast and other experiments suggests that each mutation decreases fitness in a heterozygote by about 2%. • The effect over generations of the accumulation of these deleterious mutations might be like the "copy of copy" figure above where after 100 generations the "useful" information is largely lost, if the individual alleles were not eliminated (by natural selection) from the population. 19 Rare mutations can be advantageous Some rare new alleles (mutations) are advantageous to the individual. The rare advantageous alleles - when they increase fitness - will likely increase in frequency in the population. Nylon 6: a synthetic polymer that did not exist before 1935 Flavobacterium in waste ponds now uses it as carbon source KINOSHITA et al. (1977) 6‐Aminohexanoic Acid Cyclic Dimer Hydrolase. A New Cyclic Amide Hydrolase Produced by Acromobacter guttatus KI72, European Journal of Biochemistry 80, 489-495. Kanagawa et al. (1993) Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87, Microbiology 139, 787-795 In lab, Pseudomonas aeruginosa can be selected to use same precursor as carbon source Prijambada et al. (1995) Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution, Applied and environmental microbiology 61, 2020-2022. 20 10 Germ line mutations are heritable • Somatic mutations: affect cells in the body of an organism; – not heritable • Germ-line mutations: affect gametes; heritable and relevant to evolution – heritable Recombination generates variation • Each chromosome in a human gamete has undergone about 3 crossover. • Mixes alleles between chromosome pairs Independent assortment ensures novel combinations of alleles • For n pairs of chromosomes (haploid number), independent assortment mnkes 2 combinations • n = 23 2 = 8,388,608 • Sex – “uniqueness” of the gametes that come together: < 1 / (3x23x8,388,608) < ~3 x 10-18 Linking genotype and phenotype • Genotype: the genetic make-up of an individual • Phenotype: an observable measurable characteristic of an organism 12 Genotype Testing for Allelic Variation • Most genotypes are not easily measured. • Modern molecular biological techniques simplify studies. – Gel electrophoresis – For proteins or DNA • Example shows a protein gel – Note the 3 different forms (3 alleles) – Individuals with 2 forms are heterozygotes for this gene. – Those with only one form are homozygotic. 25 Genotype Testing for HIV- Resistance • CCR5 chemokine receptor is a co-receptor for HIV-1. – Normally involved in inflammation response in white blood cells. – Needed along with CD4 for HIV to gain entry into the cell. • HIV env protein physically binds CCR5 and initiates entry mechanisms. • Mutant CCR5-D32 allele confers resistance. 26 13 Testing for the CCR5-D32 Allele with DNA Fragment Length Polymorphism • CCR5-D32 has a 32-base pair deletion that wrecks the extracellular part of the receptor. – HIV can't get in to the cell. • CCR5 genotypes can be determined by gel electrophoresis of DNA from the humans. – Figure shows PCR amplified DNA run on a gel. – Then cut with a restriction enzyme. 27 Calculating Allele Frequencies • To estimate the 43 individuals tested by genetic variation in a gel electrophoresis population, the for CCR5+ or frequencies of each CCR5-D32 allele are calculated. 86 total alleles – Example: D32 (humans are frequency in the Ashkenazi population diploid) of Europe. 18 alleles were D32 18/86 = 0.209 (20.9%) 68 alleles were CCR5+ 68/86 = 0.791 (79.1%) 28 14 Alternative Method for Calculation • An alternative method would be to calculate the allele frequencies from the genotypes of the individuals. Genotype frequencies: + / + + / D32 D32 / D32 26 / 43 16 /43 1 / 43 = 0.605 = 0.372 = 0.023 Allelic frequencies: CCR5+ allele = 0.605 + 1/2 (0.372) = 0.791 (79.1%) CCR5-D32 = 0.023 + 1/2 (0.372) = 0.209 (20.9%) 29 Simple polymorphisms can produce differences in phenotype Sometimes a single genotype can produce multiple phenotypes Polyphenic trait: single genotype produces multiple phenotypes depending on environment (nutrient dependent in this case) Environmental influences on gene expression • Phenotypic plasticity: changes in phenotype produced by a single genotype in different environments – Tailors organism to environment • Gene expression often influenced by signals from the environment – Allows match to environmental circumstances Quantitative traits influenced by genes and the environment Quantitative traits influenced by multiple Looks continuous (non-discrete!) Francis Galton (1822-19Generates a normal distribution • Multiple alleles for height • 3 main alleles for skin color Cystic fibrosis • Most common lethal genetic disease among U.S. Caucasians. Thick mucus in bronchial passageways and pancreatic ducts interferes with the functioning of these organs. • Defect lies in a chloride ion transport protein within plasma membranes. When chloride passes through, water normally follows. • In cystic fibrosis patients, a lack of water following through results in the thick mucus. • The gene for the defect is on chromosome 7. 34 Most Natural Populations are Genetically Diverse DNA electrophoresis studies of the cystic fibrosis locus • Locus on chromosome 7 • Encodes a transmembrane protein called CFTR CFTR enables cells of the lung to ingest and destroy bacteria. Homozygous CFTR loss-of-function mutations suffer chronic Pseudomonas aeruginosa infections. – Leads to lung damage • Geneticists have sequenced the DNA for CFTR in over 15,000 cystic fibrosis patients. 35 Genetically Diversity at the CFTR Locus Graph shows the abundance and location of loss-of- function mutations in the CFTR gene. Over 500 different mutations have been found. 36 18 11:22 Welcome to Evolution 3303 “It is understandable when a child is afraid of the dark; not so, for a grown man to be frightened of the light” - Plato 1 Biol 3303 Evolution John Wise, Ph.D. • Office: DLS Room 234 • Tel.: 214-768-3426 • Email: firstname.lastname@example.org • Office hours: by appointment • Ask questions! • Come visit me 2 1 11:22 Biol 3303 Evolution The Course T-Th, 8:00 to 9:20 am, DLS 110 • Text: EVOLUTION – MAKING SENSE OF LIFE, 1st Edition by Carl Zimmer and Douglas J. Emlen Roberts and Company Publishers, Inc. Colorado, USA ISBN 978-1-936221-17-2 (hardcover) or ISBN 978-1-936221-36-3 (paperback) • Web pages – – PBS Evolution (a great web site) http://www.pbs.org/wgbh/evolution/ – http://courses.smu.edu – this course 3 Biol 3303 Evolution The Course • Grading: – 2 exams given (100 pts each) – Final (100 points) – Term paper (100 points) – Course grade equals sum of points (total of 400 pts possible) • My Powerpoint file outlines will usually be available on Blackboard 4 2 11:22 Biol 3303 Evolution Term Paper • Suggested topics in syllabus • You may write on your own topic, but you must get the topic “OK’d” by me • 1 page outline due on 3/1/16 • Paper due on 4/5/16 • You must follow the format requirements given in the syllabus (single-spaced, etc.) 5 Biological evolution • Any change in the inherited traits of a population that occurs from one generation to the next – “Descent with modification over generations” THE ORIGIN OF SPECIES (1859) C. Darwin – Driving force “Natural selection” • hereditary variations for those best adapted for reproduction 6 11:22 Evolution explains the diversity of life 7 Understanding evolution has practical implications How do pathogens become drug resistant? What is the source of new pathogens? 8 11:22 Evolution case studies • Whales: mammals gone to sea • Viruses: the deadly escape artists 9 How do we know whales are mammals? • Whales share many characteristics with mammals • Synapomorphies – traits that are “the same” or shared with common ancestors – Mammary glands – Three middle ear bones – Hair (in developing embryos) • Similarities with fish arose through convergent evolution – independent origin of similar traits in separate lineages 10 5 11:22 Fossil whales share synapomorphies with modern cetaceans http://www.pbs.org/wgbh/evolution/library/11/2/e_s_3.html Videos:PBS videos1 / evidenceforevolution/ EvolvingIdeas How Do We KnowEvolutionHappens_e_s_3_300.mov7min D:\Pbs_Videos_2\DeepTime_HistoryofLife\WhaleEvolution_l_034_05_300.mov5 min(startat 4:20) Fossils reveal links to land mammals • Shape of astragalus connects to artiodactyls 12 6 11:22 Fossil sequence documents transition from land to water 13 Documenting the transition from land to water Two types of very strong physical evidence • Isotopic analysis of fossil teeth • Fossil analysis of hindlimb loss Indohyus http://www.newscientist.com/article/dn13110-deerlike-fossil-is-a-missing-link-in- whale-evolution.html#.VLaApCvF_To 14 11:22 Isotopic analysis of fossil teeth • Terrestrial animals drink freshwater; marine animals drink saltwater 18 16 • O/ O ratio higher in saltwater – Higher ratio in teeth of marine animals 15 Fossils document hindlimb loss • Simplification of the pelvis 16 11:22 Changes in gene expression led to hindlimb loss • Hindlimbs begin to form but do not fully develop • Evolution of bodies – changes in development 17 Research gives more clues about whale evolution • Loss of teeth in baleen whales • Evolution of brain size and complexity • Whale diversity over evolutionary time http://www.scientificamerican.com/blog/post/are-whales18marter-than-we-are/?id=are-whales-smarter- than-we-are 11:22 Baleen whales lost teeth • Ancestors of all modern whales had teeth – Also produced small patches of baleen • Baleen completely replaced teeth in Mysticetes – Genes for building teeth disabled 19 Brain size and complexity the result of natural selection • Sociality promoted the evolution of large brains – Form lasting alliances – Competition for mates – Complex communication • Humans and whales – Cultural learning • Orca species teach hunting skills to young 20 11:22 Historical diversity tracks ecological changes to food web • More diatoms – more whale diversity? 21 Small populations put some cetaceans at risk of extinction 22 11:22 2009 H1N1 Flu Outbreak • Spread worldwide in a matter of weeks – First noticed in Mexico • 16,000 deaths in U.S. • Evolutionary biologists helped solve the mystery of its appearance 23 Flu life cycle 24 11:22 • Eight RNAs Vaccine design – 11 genes Part of flu vaccine; primes immune system5 antigenic sites on hemagglutinin 25 Why do new flu vaccines need to be made each year? • Mutations may be harmful or beneficial • Some mutations allow the virus to escape immune system memory cells 26 13 11:22 Viral strains with beneficial mutations increase in frequency through natural selection - Viral strain no longer recognized by immune system - Requires new vaccine 27 • Experiments with mice demonstrate viral evolution 28 14 11:22 Viral reassortment can lead to devastating consequences • Shuffling of the 8 RNAs – Can occur when one cell is infected by >1 virus – Rare • Immune system cannot recognize new surface proteins • New strains can cause significant mortality • Pandemic flus: – Spanish flu (1918) • 50-100 mio dead / 50% lethality – Asian Flu (1957-58) – Hong Kong Flu (1968-69) 29 The 2009 outbreak was the result of reassortment • Pig infected by bird, swine and human flu • New infection with Eurasian avian • New reassortment with Eurasian N1 New H1N1 flu 30 11:22 • Molecular clock suggests virus went undetected for months • May not have originated in Mexico 31 Evolution in the HIV system Four steps: 1. Reverse transcriptase errors produce variation in the HIV population (mutations). 2. Mutations are inherited by following virusesions of 3. treatment, some mutations (in RT) reproduce; others fail to reproduce. 4. With AZT present, RT mutations conferring resistance persist while sensitive strains die out 32 16 11:22 Another example: Multidrug-resistant tuberculosis http://www.pbs.org/wgbh/evolution/library/11/2/e_s_6.html • Now_e_s_6_300.mov 6.5 minvolution matters\Evolving Ideas Why Does Evolution Matter 33 Common misconceptions about evolution 34 17 11:22 Evolution is “just” a theory • Scientific theories backed by multiple lines of evidence – Provide overarching explanation for major aspects of natural world • Other scientific theories – Gravity – Plate tectonics – Germ theory • Evolutionary theory overwhelmingly accepted by scientists 35 Evolutionary biologists understand everything about the history of life • Not everything is known • Biologists continually discover new aspects of life – So far, all evidence fits within context of evolution 36 11:22 Evolution explains the origin of life • Evolution deals with how life has changed after it originated • Other scientific fields address the origin of life Google: – Prebiotic evolution – Origin of life research – Black smokers 37 Evolutionary biologists search for missing links • Biologists expect the fossil record to be incomplete – Finding direct ancestors is unlikely • Available evidence strongly supports relationships between current and past species – Relationships shed light on how traits evolved 38 11:22 Evolution violates the second law of thermodynamics • Holds that disorder increases in closed systems – Earth is not a closed system – Sun provides constant input of energy 39 Evolution is natural selection • Natural selection is a mechanism of evolutionary change • Other mechanisms: – Genetic drift – Sexual selection 40 11:22 Evolution is entirely random • Evolution includes random and non-random components – Mutations are random – Selection is the non-random spread of particular mutations • Convergent evolution demonstrates that evolution is non-random – Phenotypes are predictable when environments are similar 41 Organisms evolve adaptations they “need” • Evolution cannot identify needs – Mutations do not occur because they would be adaptive in an environment – If beneficial mutations happen to occur they may increase in frequency through selection 42 11:22 Evolution is a march of progress • Evolution is not ladder-like – New species result from branching events 43 Evolution always moves from simple to complex • Evolution can also move from complex to simple – e.g. mitochondria evolved from free-living bacteria – Tape worms have no digestive system 44 11:22 Evolution results from individuals adapting to environment • Evolution only works on inherited traits – Acquired changes are not passed to offspring • Populations evolve; individuals do not – Evolution results from changes in allele frequencies 45 Organisms are perfectly adapted to their environment • Natural selection can only work with available variation – Constrained by physics and development • Many traits involved in trade-offs – e.g. human brain size / birth canal size / jaw size 46 11:22 Evolution happens for the good of the species • Evolution selects traits that are beneficial for individuals or their genes – Traits that are bad for individuals (or genes) will not be selected even if they are good for the species 47 Evolution promotes selfishness and cruelty • Natural selection favors traits that increase reproductive success – Different conditions select for different traits – Cooperative traits are beneficial under some conditions 48 11:22 Evolution seeks peaceful harmony in nature • Natural selection favors traits that increase reproductive success – Can result in exploitation – Can result in cooperation 49 Life can be divided into higher and lower forms • All of life is adapted to the environment in numerous ways – Environments differ so adaptations differ – One adaptation is not “superior” to another adaptation 50 11:22 Evolution has produced a stable diversity of life • Extinction means diversity is not stable – 99% of all species that ever existed are extinct http://www.biologicaldiversity.o stainability/extinction_and_pop ulation_graph.html 51 One cannot be religious and scientific • Science and evolutionary theory are not mutually exclusive of religion. • A few examples follow 52 26 11:22 “I am a creationist and an evolutionist.” Theodosius Dobzhansky: “It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God's, or Nature's, method of Creation.” – from "Nothing in biology makes sense except in the light of evolution" (Am. Biol. Teach. 35, 125–129; 1973) Dobzhansky argued that "the Creator has created the living world not by caprice (supernatural fiat) but by evolution propelled by natural selection". 53 Accepting both God and Science Dr. Francis Collins is the director of the National Institutes of Health and is an evangelical Christian biologist. “the evidence that we are all descended from a common ancestor is overwhelming. Some might wish that not to be so. It is so. Does this conflict with Genesis 1 and 2? I don't believe it does.” 54 11:22 Francisco Ayala – Former Dominican Priest – Student of Theodosius Dobzhansky – Evolutionary Biologist and Philosopher at UC Irvine – National Academy of Science Member – >1000 publications! “Evolution is more consistent with belief in a personal god than intelligent design. If God has designed organisms, he has a lot to account for” – Sadism in parasites – 20% of pregnancies result in spontaneous abortion Don’t teach both evolution and creationism: – “We don’t teach alchemy along with chemistry. We don’t teach witchcraft along with medicine. We don’t teach astrology with astronomy.” 55 A Recommended Book on Evolution and Religion: FINDING DARWIN'S GOD: A SCIENTIST'S SEARCH FOR COMMON GROUND BETWEEN GOD AND EVOLUTION by Kenneth Miller – Professor of Biology Brown University http://www.brown.edu/Administration/Brown_Alumni_Magazine/00/11-99/features/darwin.html See also: http://www.millerandlevine.com/km/fdg/ 56 56 28 11:22 Rejecting God because of Science Dawkins argues that belief in a supernatural creator qualifies as a delusion. He has no more hard evidence that God does not exist than Intelligent Design has scientific evidence that God does exist. Each conclusion ultimately comes down a leap of faith. This leap takes you out of the natural world and science altogether and brings you into a matter of faith and belief. 57 Evolution and Religion: Is there a conflict? For more see http://ncseweb.org/media/voices/religion/ See also http://ncse.com/religion/science-religion-l58ks 11:22 Homework: What is Science? Information sheet to download on the Blackboard site – "What is Science.pdf". Please know this material. 59 Chapter 3 How the rocks reveal the history of life Darwin recognized that evolution required an old earth • Darwin argued that earth could be billions of years old • Disputed by Lord Kelvin (William Thomson 1862) – Proposed earth was no more than 20 million years old based on the temperature of rocks – Calculations later proven to be flawed • Contradicts Bishop James Ussher (1650) – Claimed the Earth is 6014 years old – Based on genealogies of the “Old Testament” Radiometric dating indicates that the earth is 4.6 billion years old E:\Pbs_Videos_2\DeepTime_History of Life\Radiometric Dating_l_033_01_300.mov Most organisms don’t fossilize http://www.pbs.org/wgbh/evolution/library/04/3/l_043_01.html Pbs_Videos_1\EvidenceforEvoluti2.5 minminga Fossil_l_043_01_300.mov 2 Occasionally soft tissues fossilize • Burgess shale 505 million years ago ~65,000 specimens ~93 species • Shows early animal body types – Some very bizarre Fossils provide clues about behavior A. Live birth in ichthyosaurs B. Predation C. Herding tracks D. Nesting site of maiasaurs (parental care!) 3 Fossils provide clues about development • Inferring developmental pathways for growth from large sets of same species Scanning electron microscopy provides evidence of cellular structure • SEM structures of melanosomes suggests striking plumage in Anchiornis huxleyi CT scans help determine function of hadrosaur crest • Crest connected to nasal cavity – Sound generated by blowing air • Ears tuned to this frequency Biomarkers reveal traces of life • Biomarker: distinctive molecules only produced through biological activity • Okenane is a carotenoid pigment • Only made by purple sulfur bacteria • Found in 1.64 byo rocks • Inference – purple sulfur bacteria were there Carbon isotopic signatures used to infer diet of early hominins • C plants (grasses) have lower 13C than C plants 4 3 – C 13 14 ratio used to infer types of plants eaten – Browsers – above ground level – Grazers – from the ground – Early hominins ate some grasses Scientists search for evidence of life in old rocks • Earliest life unlikely to be preserved in fossils – Early history of Earth too violent – Most common early Earth crust material is zircon • Presence of carbon in early rocks suggests life Trapped carbon in – Isotopic signature distinguishes from zircon crystal lifeless carbon sources • Carbon from nonliving sources has higher 1C/ C ratio (photosynthesis doesn’t like 1C) • Light Carbon found in 3.7 byo zircon 6 Earliest signs of life • Oldest evidence of life dates to 3.7 bya – Carbon contained in rocks – Claim is controversial • Oldest stromatolite (bacteria) fossils date to 3.45 bya Bottom: Fossil stromatolites How do early organisms fit in the tree of life? Earliest fossils: ~1.8 bya Earliest fossils: potentially 3.45 byo; abundant by ~2.6 bya, corresponding to rise in oxygen Earliest fossils: ~3.5 bya 7 Origin of multicellularity a major transition in history of life • Evolved independently in different lineages • Extant organisms provide clues about origin of multicellularity • Bacterial communities (biofilms) • coalesce into a slug and crawl away and produceals spores Oldest fossils of multicellular life date back 2.1 billion years • From Gabon, West Africa • Unclear whether bacteria, archaea or eukarya Eukaryotic multicellular life • Earliest fossils of algae date to 1.6 bya – Red algae: 1.2 bya – Green algae: 750 mya Red algae fossil; 1.2 bya The dawn of animals • Early animal life resemble sponges – Oldest fossils 650 myo – Biomarkers in 650 myo rocks (cholesterol specific to sponges) – right shows serial cross-sections (radial symmetry) Search for early animals can be controversial Animal embryos or animal-like “cysts”? -from 580 myo rocks (Doushantuo Formation) Ediacaran fauna • Diverse and unique animals dominated the oceans from 575 – 535 mya • Many hard to place taxonomically – most (all?) died out • WerKimberella – had a clam-like rasp Dickensonia was bilateral Animals? 10 Evolution of Ediacaran fauna Some currently existing lineages recognizable during the early Cambrian Burgess Shale Fauna - Early Cambrian: 542 – 511 mya E:\Teaching\Pbs_Videos_2\DeepTime_History of Life\The Cambrian Explosion_l_034_02_300.mov Books to read Chordates emerged during early Cambrian Haikouichthys – small fish like with notochord and gills (525 mya) Dunkleosteus – bony vertebrate predator (380 mya) Transition from ocean to land a major event in evolution • Prokaryotes colonized terrestrial environments first – Fossils date to 2.6 bya • Terrestrial animals, plants, and fungi, appeared much later First terrestrial plant and fungal life • Oldest terrestrial plant fossils are 475 myo – Early plants resembled mosses and liverworts • Large forest ecosystems within 100 million years • Fungi appear ~ 400 mya – Found associated with plants • Oldest gymnosperms ~319 mya • Oldest flowering plants ~160 mya Oldest land animal fossil • 428 myo millipede Pneumodesmus newmani http://www.explicame-evolucion.com/wp- wmani21.jpgoads/2011/07/Pneumodesmus_ne First terrestrial vertebrates tetrapods - vertebrates with legs • Oldest trackways (possible tetrapods) date to 390 mya • Oldest fossils of tetrapods date to 370 mya (Silvanerpeton) Familiar forms of life did not emerge until recently • 350 million years ago many currently existing lineages had yet to evolve – Teleost fish – Mammals – Birds – Flowering plants Evolution of mammals • Mammals evolved from synapsids – Dominant vertebrates around 280 myo – First mammals emerged 150 mya Diversification of mammals • Mammals diversified after dinosaurs went extinct (~65 mya) • Whales, bats, and primates all emerged around 50 mya Oldest biped hominid – – Sahelanthropus – 7 mya – Found in Sahara desert Oldest modern human fossils are ~200,000 years old Evolution of other major lineages • Birds: ~150 mya – Descendants of dinosaurs • Flowering plants: ~132 mya – Grasses did not diversify until ~20 mya • Insects: emerged ~400 mya – most current lineages appear much later 2/3/2016 Chapter 4 The tree of life: how biologists use phylogeny to reconstruct the deep past Darwin viewed evolution as a branching process “As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ramifications.” – Darwin, 1859 From Notebook B, pg. 36 - 1837 1 2/3/2016 Phylogeny: A visual representation of the evolutionary history of populations, genes, or species. A-C. Mating of individuals D. Extended to populations E. Species level – linked populations F. Species sometimes divide into two populations that no longer interbreed A phylogeny is similar to a family tree 2/3/2016 Reading a phylogenetic tree Taxa can be rotated around nodes and still depict the same relationships Phylogenies may be drawn in different styles 2/3/2016 No currently existing species is ancestral to any other Trees can be drawn with fewer species 2/3/2016 Life is organized in a nested hierarchy Taxonomic units legitimate only if they represent a clade Clades are monophyletic groups - related by direct descent 2/3/2016 Some Linnean classifications are not monophyletic Linnean Modern Key Concepts • New lines of evidence suggest some commonly used taxon names should be revised to reflect evolutionary history 2/3/2016 Reconstruction of phylogenies is based on analysis of characters A – 12 characters scored “0” or “1” B – Outgroup is creodont – but no info on kidneys, etc. C – Character of creodont- carnivore ancestor inferred • Synapomorphies now quantitated Clades are determined by synapomorphies Shared similarities due to common descent Now build the tree Dercharacters are listed by their number (see Table A) Polytomy – dogs and raccoons lack that wouldhy separate them from the third branch 7 2/3/2016 Not all traits are similar due to common descent • Homoplasy: character state similarity not due to common descent – Convergent evolution: independent evolution of similar trait – Evolutionary reversals: reversion back to an ancestral character state Homoplasies can be misleading in reconstruction of phylogenies Does not fit with cat/hyena clade Contradicts many other character similarities 2/3/2016 Principle of parsimony used to find tree that is most likely to be correct Computer programs with 19 characters finds 3 trees cannot be differentiated – all require 31 steps (branches + Equally parsimonious (least required steps) Can make a consensus tree with polytomies to represent all three solutions (B) Summary so far • Phylogenies are created by identifying synapomorphies • Homoplasy can create the mistaken impression that two species are closely related when they are not 9 2/3/2016 Fossils can be used to constrain divergence times A – Some phylogeny is organismseen B –found related to Ys TelX and Y must bestors older than 50 my. C & D – But with just one fossil, we can’t tell these two apart. New fossil finds are required Fins to limbs: homology through time Coelacanths are one of the closest living relatives of tetrapods 10 2/3/2016 Coelacanth fins are homologous to tetrapod forelimb Ray finned fishes (teleosts) finned fishes (coelacanths) added bones and muscles Fossil record should document transition from fins to forelimbs Phylogenies generate hypotheses Transitional tetrapods should be found in mid-Devonian rocks 2/3/2016 Scientists predicted where transitional fossils would be found • Searched mid-Devonian rocks in Northern Canada – Appropriate age and habitat Tiktaalik: transitional fossil between fish and tetrapods was found in mid-Devonian rocks Crucial test of Evolutionary Theory – a certain event occurred at a specific time and the Earth produced the fossil evidence. 2/3/2016 Tiktaalik forelimbs share more homologies with tetrapods One bone - humerus Two bones radius and ulna Lots of little bones fingersones and E:\Pbs_Videos_2\DeepTime_History of Life\Fish with Fingers_l_034_03_300.mov Phylogeny reveals how tetrapod traits evolved over time Lots more species and lots more details are known 2/3/2016 Homology can be obvious…or not Homology between human (left) and chimpanzee (right) hands is obvious Reptilian jaw bones are homologous to mammalian inner ear bones Fossils and phylogeny document transition of bones from jaw to ear 2/3/2016 Birds are dinosaurs: tracking the evolution of feathers and flight Archaeopteryx, discovered in 1860, dates to 145 mya Feathers evolved before flight 2/3/2016 Feathers originally involved in other functions Exaptation: natural selection co-opts a trait for a new function: feathers for warmth or attracting mates become useful for flight Feather attachments Velulnaaptor on Velociraptor bones Turkey ulna 16 2/3/2016 Dinosaur nesting behavior Darwin proposed that humans most closely related to African apes • Fossil record should document transition to to unique human traits – Bipedality – Larger brain size – Smaller canine teeth • Coccyx bones of monkeyand tailed Human ancestor probably had a tail 2/3/2016 Phylogeny reveals transitions Transition to bipedality • Appears to have evolved before larger brain – Position of foramen magnum – Weight bearing stance – Short, stiff toes E:\Pbs_Videos_1\Human Evolutionhttp://users.rcn.com/jkimball.ma.ultra Tall_l_071_02_300.mov net/BiologyPages/P/Primates.html 2/3/2016 Ardipithecus adapted t
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