BILD 3 Lectures 1-5 Notes

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Biology/Lower Division
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Krystal Rypien

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BILD 3 | Organismic and Evolutionary Biology Lectures 1-5 | Notes Darwin + Natural Selection | Lecture 1 Charles Darwin, 1809-1882—the father of modern evolutionary theory  Origin of Species by Natural Selection, 1859 o All organisms evolved from a common ancestor, but became modified over time—evolution as descent with modification  Descent with modification—Earth’s many species are descendants of ancestral species that were different from the present-day species  Evolution—change in the genetic composition of a population from generation to generation o Mechanism: natural selection  Natural selection explains the observable patterns of evolution  His book profoundly challenged prevailing world views, ushering in a scientific revolution—the era of evolutionary biology  Evolution as a pattern and a process Old World View  Scientific thinking in Europe in the 1880s espoused a “special creation”, religiously centered, view of life o All species were created by God and were therefore perfect o Species do not change; species were created independently o The world is too young to allow for the long time it would take for such evolution to occur in species  Evolution, that, is not a new idea  600-400 BC: Ancient Greek philosophers (Anaximander of Miletus, Empedocles) o Several suggested that life might have changed gradually over time o Aristotle—viewed species as fixed and unchanging, each form of life was perfect and permanently allotted a rung on the scale of nature  400-300 BC: Zhuangzi, Chinese Taoist philosopher o Space and nature are constantly changing  800-900: Islamic philosophers (al-Jahiz, Ibn Khaldun) o Struggle for existence, compete to survive, food chain Changes in thinking  Changes in people’s views on natural history and natural selection are brought about by developments in Classification, Geology, Paleontology, Economics, and Evolution  Darwin’s revolutionary proposal was developed over time and influenced by his travels and the works of others Classification | Charles Linnaeus, 1707-1778  Swedish physician and botanist  He developed 2-part binomial format for naming species, biological nomenclature that is still used today  Classified organisms into nested hierarchal categories—grouped similar species into increasingly general categories  However being pre-Darwinian, the groupings were based not on evolutionary kinship but to the divine pattern of their creation—divine plan Nested, Hierarchal Categories (Linnaeus)  3 Kingdoms—Animal, Vegetable, Mineral  Kingdom: Animal  Class: Mammal  Order: Primates  Genus: Homo  Species: Sapiens Nested, Hierarchal Categories (Modern)  3 added classifications: Domain, Phylum, Family  Now based on evolutionary relationships, not divine order Paleontology | George Cuvier, 1769-1832  Studied fossils and rock layer  Demonstrated that the Earth’s biota changed over time  Established extinction as a fact (mechanism= caused by catastrophe)  1 to speculate on age of reptiles before mammals (dinosaurs)  Favored catastrophe theory over gradual evolution Paleontology | Mary Anning, 1799-1847  Discovered the first plesiosaur and the first ichthyosaur fossils  Contributed to Cuvier’s hypothesis that giant reptile-like creatures ruled the earth before mammals Geology | James Hutton, 1726-1797  Very slow geological processes observed in modern day must have been operating in the past—uniformitarianism  Gradualism—mm  His ideas suggested that the Earth was actually much older that previously thought Geology | Charles Lyell, 1779-1875  Popularized Hutton’s idea of uniformitarianism, as originally put forth by Hutton, and provided more evidence for the idea  Close and influential friend of Darwin  Saw geologic change as the steady accumulation of small changes over enormously long spans of time Evolution | Lamarck, 1744-1829  Described mechanism to explain why organisms in fossil record are different than present day organisms: inheritance of acquired traits o Use/Disuse of a feature can lead to change within an organisms lifetime o These acquired changes are inherited  First to suggest a mechanism (although incorrect) of how species change over time through evolution  Example of Lamarckian evolution: giraffe’s neck as elongated by stretching to reach leaves on tree branches Economics | Thomas Malthus, 1766-1834  Essay on the Principle of Population, 1798  Human populations periodically produce too many offspring leading to widespread famine  Outliving our means, so there will always be people who live in poverty, unchanging circumstances  There is a struggle to survive, favorable genes passed onto future population  Darwin recognized that favorable variations in traits would tend to be preserved, and unfavorable traits destroyed—Natural Selection Charles Darwin | 1809-1882 Evolution by Natural Selection  Son of an English doctor, dropped out of medical school’ studied theology at Cambridge  Unofficial naturalist on the HMS Beagle, 1831-1836 o Voyage changed Darwin’s life, it was the inspiration for his book  Natural History was a passionate hobby of his, as a wealthy man he didn’t have to have a real job Voyage of the HMS Beagle, 1831-1836  The great adventure of Darwin’s life, he collected animals, plants, fossils, and made many observations  Six important ports of call 1. Cape Verde Islands o Darwin found a ring of white sedimentary rock containing marine shells around Santiago about 15m above sea level o Evidence that the sea level changed over time 2. Brazil o Darwin’s first exposure to wet tropical environments with their astounding diversity o Organisms here resembled species in temperate portions of South America that Darwin later visited 3. Punta Alta, Argentina o Discovered the bones of extinct giant mammals in the cliffs, similar to some animals still living in the area o Recognized similarity to extant (living) forms 4. Falkland Islands o Curious about how Falkland’s fox go onto these islands, must have been different in the past, maybe connected to the mainland by a land bridge o Also found brachiopod marine fossils in the rocks—clues to life in the distant past on the Islands 5. Chile o Darwin found fossil marine shells in sedimentary rock at 12,000 ft., meaning that the mountains had once been at the edge of the ocean o Witnessed volcanic eruption and a massive earthquake that raised portions of the coastal shelf by 8ft o Saw portions of the coastal shelf driven up 8 ft. into the air o Provided Darwin with confirmation of Lyell’s theory of uniformitarianism (change over time, the same process that occurs to make the landscape and earth what is now are also occurring today and causing more change) 6. Galapagos Islands o Galapagos Islands are an important stop, although Darwin does not realize this at the time o He was impressed by the variety of animal and plant species and the geology o Darwin realized that the different islands within the archipelago supported distinct species and subspecies o Galapagos tortoises with their different shells After the Voyage  Darwin returned to England in 1836, the Origin of Species published in 1859  What did he do for 23 years? o In the 23 years since his trip on the HMS Beagle, Darwin developed and gathered evidence for a mechanism for evolution—natural selection Darwin Studied Barnacles, 1846-1854  Created an exhaustive taxonomy based on comparative anatomy; showed variation within and between species  Empirical means to tests his views on species Darwin bred pigeons, 1855  Different kinds of pigeons could be created from a common ancestor  Traits were selected for, pigeon breeders had been doing this for years o Example, like the artificial selection that occurs in food crops Darwin studied how organisms disperse  How could plants colonize a new volcanic islands  Darwin conducted experiments on seed dispersal, seeds in seawater  Concluded that plants could disperse on their own, cross oceans and colonize new volcanic islands Darwin studied Galapagos Finches  Darwin collected a number of bird on the Galapagos Islands that had dramatically different breaks—he assumed they were different species of blackbirds, wrens, and finches o Huge variations in bill size and shape  Gould, an ornithologist, discovered the birds were all finches  There are variations within the species that adapts to and accommodates the different circumstances of the different islands, adaptation to allow for best chance of survival Alfred Russell Wallace  Wallace left school at 14 to make money  Amateur naturalist who collected beetles as a hobby  He and a friend hatched a plan to travel to the Amazon and collect exotic animals to sell as novelties to collectors in England o Spent four years, 1848-1852, collecting exotic organisms in the Amazon o Endured harsh conditions—heat, tropical disease, foreign cultures, rotting specimens, boast sank on the way back and they lost specimens o Saved a diary, some sketches, and notes—observations of the wide variety of species they had seen and collected  Second voyage in the Malay Archipelago, 1854-1861 Wallace observed variation within and between species  Wallace was developing his own idea about how the diversity of life came into being Wallace and Darwin  In 1858, Wallace write a paper that described the process of evolution by natural selection o Sent manuscript to Darwin, who then sent it on to Lyell  Darwin was terrified about getting scooped  Lyell suggested they present their works simultaneously in July 1858 o Neither Darwin or Wallace in attendance o Muted public reaction  Darwin published Origin on Species by Means of Natural Selection in 1859 o Huge success  History largely credits Darwin for the idea of natural selection o Wallace, upon his return to England I 1862, was one of Darwin’s staunchest defenders for the case of natural selection Origin of Species  All organisms evolved from a common ancestor, but became modified over time— descent with modification  Mechanism—natural selection 5 Facts, 3 Inferences  Fact: If all individuals that were born reproduced successfully, population size would increase exponentially  Fact: Population size is normally stable, excepting minor annual fluctuations and occasional major fluctuations  Fact: Natural resources are limited o Inference: Since more individuals are produced than can be supported by available resources, but population size remains stable, it means there must be a struggle for existence o Inference: Survival in the struggle for existence is not random, but depends on the heredity constitution of the remaining individuals. This unequal survival constitutes the process of survival of the fittest  Fact: No two individuals are exactly the same  Fact: Much of this variation is heritable o Inference: Over generations, natural selection will lead to a gradual change in populations (evolution and the production of new species) How were Darwin’s ideas accepted?  Descent with modification was widely accepted soon after publication o Easily reconciled with religious views o Data in support was overwhelming  Natural Selection—universally rejected for 50-60 years Why the idea of natural selection was rejected  Seemed to preclude religious belief of divine purpose  Earth wasn’t seen as old enough for natural selection to create the extent of diversity we see today, thought to be 10-100 millions years old  No comprehensive understanding of inheritance o Blending inheritance—inherited characteristics are mixed, like __ o Lamarck: source of variation was inheritance of characteristics acquired in response to environmental conditions How those arguments were countered  Earth is really old o Discovery of radioactivity, 1868, and radioactive dating o Current estimates for Earth’s age: 4.6 billion years old  Better understanding of genetics o Gregor Mendel, 1822-1884 o Mendel’s work on peas published in 1865, discovered in 1900 o Parents pass discrete units of info to offspring o August Weismann, 1834-1914 o Heritable traits pass from generation to generation via material in nuclei of cells o Inheritance only take place by means of the germ cells/gametes. Other cells of the body do not function as agent of hereditary o Discredits Lamarck’s ideas  By early 1900s, natural selection was widely accepted in the scientific community Whales (Cetaceans) | L2 Evidence of Evolution  Transition from land mammal to whales Whales (Cetaceans)  85 living species of whales and dolphins, cetaceans  Whales belong to the mammal category Where did whales come from?  Darwin’s theory that whales came about through natural selection, evolving from land mammals to aquatic, becoming o “…More and more aquatic in their structure and habits, with larger and larger mouths, till a creature was produced as monstrous as a whale”  Hypothesis: Whales descended from a common ancestor—Creodont—with carnivores 150 million years ago (MYA)  Evidence that demonstrates the occurrence of evolution o Fossil Record o Homology (structural, developmental, and molecular) o Direct observations in the lab and field Evolution is genetic change over time  Microevolution—change in the genetic composition of a population across generations, short time scales o Hypothetical population of beetles, green v. brown beetles  Macroevolution—evolution occurring above the species level, long time scales Fossils  Fossil—any trace of organisms that lived in the past  Fossil record incomplete o Fossils only form under certain environments/conditions and only certain organism, usually those with hard skeletons or shells  Teeth, bones, petrified trees, leaves o Must be quickly preserved, before decay begins, into order to fossilize  Tree sap, layers of sediment  Living Fossil—any organism showing no morphological change over very long time periods; usually no close living relatives o Gingko tree leaves, 170 mya o Horseshoe crab, 445 mya Fossils can be used to test evolutionary hypothesis  Fossil sequences reveal timing of evolutionary events  Evidence of organisms that left no living descendant  Episodes of diversification and extinction  Historical distributions Extinction  Irish Elk: last lived 7700 years ago in Siberia, is now extinct: Cuvier, 1812  Extinct organisms show that the history of life changes, not immutable Succession  Fossils from one region are similar to extant organisms from that same region o Example: Australian fossils are more similar to Australian organisms than they are to European organisms  Darwin noted similar patterns when he visited South America o Extant pygmy armadillo / fossils of extinct giant armadillo like creatures  Evidence of evolution, common features for from common ancestor Transitional Forms  Organisms that have characteristics of both ancestral and modern forms  Ex: Sphecomyrma is a transitional form between wasps and ants Fossil Evidence for Evolution  Early cetaceans should show a mix of features immediate between modern whales and terrestrial mammals  Features of modern whales we can look for in the fossil record o Missing hind limbs o Flipper-like front limbs o Uniform peg-like teeth o Nostrils on top of head, movement of nostrils to top of skull Pakicetus  Discovered in 1983 in Pakistan  50 mya  Whale like teeth, hind limbs and hooves, lived on land Dorudon  Discovered in 1936 in Pakistan  36 mya  Front flippers, tail with long extended vertical column, tiny hind legs  Big jump from Pakicetus to next phase, jump from land to water Ambulocetus natans—the walking whale  Transitional fossil, 48 mya  Discovered in 1994  Whale like teeth, beginning of nostril transitions, paddle with hind limbs, otter swim  Fossil whales not necessarily direct descendants of modern whales o Transitional forms were more likely o Shared a common ancestor 55 mya, slow gradual change Archaeopteryx  Transitional form between dinosaurs and birds from the late Jurassic, 150 mya  Size of crow, skeleton like dinosaur but had feathers and wings, dinosaur teeth Transitional forms are just one branch on an evolutionary tree  Recently scientists in China have discovered 4-winged fossils, 130 mya Homology  Similarity due to inheritance of traits from a common ancestor  Ex: gingko and oak tree leaves, wings of butterflies and dragonflies, teeth of beavers and tusks of elephants (share an ancestor with incisor teeth, different functions but derived from same ancestors) Molecular Homology  Similarities among organisms at the molecular level due to a shared ancestor  Closely relatedly species will have less DNA sequence differences than species that are more distantly related Structural Homology  Anatomical similarities due to common ancestry  Ex: mammalian forelimbs have same basic structure despite different functions  Why? Modifications of ancestral form’ Where did Whales come from?  Similarities in ankle bones link whales, hippos, and fossil cetaceans Developmental Homology  Similarities in features during development, despite differences in adults  Vertebrate embryos o All have something similar to gill slits of fishes o All have tail remnants o Because all vertebrates shared common ancestor o Ex: chick and human embryos Vestigial Organs  Functionless or rudimentary organs in one species that has important function in other species o Blind salamander with vestigial eyes o Mexican tetra and blind cave tetra o Flightless birds that still have wings  Cassowary, Great Auk, Dodo, Flightless Cormorant, Kiwi  Vestigial Organs in Humans o Goose bumps—muscles attached to hair follicles contract and make hair “stand on end”  This is useful for hirsute/hairy mammals for thermoregulation and intimidation  Not effective in humans as we don’t have enough hair o Other vestigial organs in humans: wisdom teeth, appendix, coccyx Homologs & Phylogenetic Trees Convergent Evolution  Evolution of similar features independently in different evolutionary lineages, usually from different antecedent features or by different developmental pathways  Evolution favored the features independently  Ex: bird wings and insect wings Analogous Structures  Structures that are similar due to convergent evolution, not shared evolutionary history Where do whales come from?  Multiple lines of evidence all support that whales share a common ancestor with hippos o DNA homology o Structural homology, ankle bones  Transitional fossils demonstrate a gradual change from terrestrial mammal to ocean-dwelling whale o Selective pressure of life in the ocean resulted in natural selection driving the evolution of whales Direct observations of evolution  Evolution of multi-drug resistant tuberculosis, TB (an air borne, bacterial infection of the lung)  Drug resistance o Bacteria vary in their response to drug o Some bacteria have higher survival o Can pass that trait to offspring o Bacteria population becomes resistant—evolved, genetic change over time  Evolution of pesticide resistance o Result of overuse of insecticides o Strong selection for resistant genotypes o Evolution of resistance can occur quickly o There has been an increase in the number of arthropod species known to be resistance to one or more insecticides An experimental demonstration of evolution using the flower Alpine skypilot  Observations o Tundra—large, sweet smelling flowers attract bumblebees o Timberline—small bad smelling flowers attract flies  Hypothesis—Natural selection by bumblebees has caused the tundra flowers to evolve large sizes, evidence of natural selection Artificial Selection | L3 Artificial Selection  Selective Breeding to produce populations with desirable traits o Natural selection imposed by humans for a specific goal  E.g. dogs, pigeons, cruciferous vegetables  Special type of natural selection, with humans being the acting/determining force, instead of nature Artificial Selection in Food Crops  Cruciferous vegetables bred selectively over time  Wild Mustard  Kale for leaves, Brussels Sprouts for side buds, Cabbage for tip buds, Broccoli for flowers and stems, Kohlrabi for stems How did cauliflower come to be? 1. Individuals vary (flower type)  Farmers in the Mediterranean plant only those with dense, tasty flowers and this results in genetic change over time, as a result of artificial selection 2. Individuals with certain traits selected for breeding, and therefore these individuals have greater survival rate and reproduction 3. If variation is heritable (genetic), then (over time) 4. The result is evolution Genetic Variation  Must have variation in a trait in order to have natural/artificial selection  Phenotype—the characteristics of an organism as a result of genes and the environment  Genotype—genetic composition of an organism o Phenotype: blue eyes brown eyes o Genotype: bb Bb or BB  Not all phenotypic variation is inherited o I.e. is the result of genotypic variation o Phenotype = genotype x environment  Diet, not genotype, determines the morphology of Nemoria arizonaria caterpillars o Oak flower diet v. oak leaf diet o Caterpillars look different because of their diet, not because of genetic diff o Chemicals in the oak flower make caterpillars who eat them look like oak flowers, and those who eat oak leaf look like oak tree branches o Phenotypic plasticity o Some characteristics, like height, are affected by ones environment Where Does Genetic Variation Come From? 1. Mutation—permanent alteration of DNA o Only source of new genetic variation o Has to be heritable, i.e. in germ cells that give rise to reproductive cells, to alter the population o Mutations arise from copying errors during cell division and exposure to mutagens (chemicals, radiation)  Random and unpredictable, can be beneficial, negative, or have no affect at all 2. Sexual Reproduction—reshuffles the deck and creates new genetic combinations o Independent Assortment—whether a gamete gets a maternal or paternal copy of each chromosome is random, orient in a random way o Crossing Over—recombination, produces chromosomes that carry genes derived from both parents, mix of chromosomes instead of having only paternal or only maternal o Fertilization—combines genes from different individuals Evolution by Natural Selection 1. Variation exists within a species with respect to morphology, physiology, or behavior, must have variation 2. Heritability of variation (or some amount of it), only heritable characteristics can be passed on to future generations 3. Differential survival and reproduction of phenotypes 4. Adaptation to the environment is a consequence of natural selection Fitness  The contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals  Fitness depends on an organism’s overall reproductive success compared with other organisms in the population Galapagos Islands  Located about 1000 km from the coast of Ecuador, South America o This is just a little further than the distance between SD and Reno Nevada, and the space between the island and the mainland is deep water  Terrestrial species on these islands wont have many relatives nearby  Neighboring islands will have close relatives, isolated o New terrestrial species wont arrive on these islands from the mainland often o Most islands species have had plenty of time to differentiate from their nearest living relatives Galapagos Endemics  Animals living on the Galapagos today are found nowhere else on earth—Endemic  The most famous of the endemic birds are the Galapagos/Darwin’s finches, of which there are 13 different species  Galapagos finches colonized the Galapagos Islands from the mainland about 2 mya Long term study on the Medium Ground Finch by Peter and Rosemary Grant, from Princeton University o Finch study on Daphne Major, one of the Galapagos Islands o Daphne Major—top of a small volcano o Jan to May—wet season, Jun to Dec—dry season  Finches show variation in bill depth, 1976 Heritability  Heritability (h^2)—proportion of variation in a trait that is genetic, how much of a difference between individuals can be transferred from one generation to another o Heritability = genetic variation / phenotypic variation  Estimate heritability (0-1) by measuring relationship between parents and offspring o Slope of the regression line between offspring trait value and the average parent value  Heritability asks how much genetics play a role I differences in height between people. This is not the same as asking how much genetics influence height in any one person.  Heritability is specific to a particular population in a particular environment at a particular time (because its about differences in features) 1977: A Change in the
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