Exam 1 Bio 2 Notes PDF

Exam 1: Mechanisms of Evolution ​ Origins/history of life, natural selection, systematics ​ Lecture 2 ○​ Define what is life ○​ Describe hypotheses and evidence on origins of life ○​ State the age earth, when life originated, and importance of fossils ○​...

Exam 1: Mechanisms of Evolution ​ Origins/history of life, natural selection, systematics ​ Lecture 2 ○​ Define what is life ○​ Describe hypotheses and evidence on origins of life ○​ State the age earth, when life originated, and importance of fossils ○​ Where did the first life come from? ○​ How did all the necessary parts of a living cell come together? ○​ How can non-living matter evolve? ​ Lecture 3 ○​ State the importance of fossils ○​ Explain how radio-isotopes are used for dating fossils ○​ Name factors that affect the completeness of the fossil record ​ Lecture 4 ○​ Outline the history of life via geological timescales ​ Lecture 5 ○​ Theory of Evolution ​ What is evolution? ​ What does ‘theory’ mean is biology ​ History and Charles Darwin ​ The components of organic evolution ○​ Evidence of evolutionary change ​ Fossils, biogeography, convergence, homology… ​ Lecture 6 ○​ Describe major molecular processes that underlie evolution ​ Ways species can acquire new genes and how molecular changes in genetic material is associated w evolution ○​ Define population genetics, alleles, genotypes, phenotypes ○​ Explain how the hardy-weinberg model is used to test if populations have evolved Lecture 2 (33) ​ Myiasis = invasion/infestation of vertebrate tissue (meat) by fly larvae (maggot)​ ○​ Maggots = larval stage of flies (small, worm-like organisms that feed on decaying organic matter & maggots are created when flies are attracted to meat, then flies lay eggs, then the eggs hatch into maggot within 24 hours  ○​ They feed on living or dead tissue ○​ This falls under the more positive myiasis because they are clearing out dead animals ​ Facultative myiasis =maggots develop in necrotic tissue such as foul-smelling wounds, ulcerations (especially those producing pus) ○​ Maggot therapy= introduce live disinfected/clean maggots (maintained in lab setting) into non-healing wounds to clean out necrotic tissue because maggots only eat dead tissue ○​ This process is known as debridement → the process of removing dead(necrotic) tissue to help a wound heal because you need to cut off/remove dead tissue to heal necrotic tissue. ​ History of the Earths: 4 phases ○​ (1) archean ○​ (2) proterozoic ○​ (3) phanerozoic ○​ (4) cenozoic ​ Big Bang = hypothesis of giant explosion of energy and mass and then slow accumulation and expansion of the universe ​ Origin/age of Earth = 4.55 billion years ago ​ Origins of life on Earth = 4 to 3.5 billion years ago** ​ Definition of life: metabolism, reproduction, evolution, chemical system (chemistry) ○​ Other qualities: DNA, cells, adaptation, homeostasis, & growth ​ Metabolism examples: absorption of nutrients, excretion of wastes, energy acquisition and transformation (Krebs Cycle/ transforming light (energy) into sugar), cellular synthesis ​ Reproduction examples: growth → duplication of all cellular components & division of cells ​ Evolution examples: variation, reproduction, mutation: mistakes in copying cell components ​ Do viruses have the 3 properties of life? ○​ They can reproduce and evolve, but do not have metabolism b/c they take over the cell to achieve energy ​ Origin of life/how life was created 4 stages: ○​ (1) organic molecules like nucleotides and amino acids produced prior to the existence of cells ○​ (2) nucleotides and amino acids became polymerized to form DNA, RNA, and proteins  ○​ (3) Polymers became enclosed in membranes ○​ (4) polymers enclosed in membranes acquired cellular properties ​ (1) organic molecules like nucleotides and amino acids produced prior to the existence of cells ○​ Meaning organic molecules (building blocks) were simply in the environment before life originated ○​ Conditions on early Earth probably had more spontaneous formation of organic molecules ​ This spontaneous formation is known as the prebiotic (primordial) soup ​ chemical/atoms bouncing on each other, forming new chemicals, turning into different chemicals resulting in diversity of compounds (important for life formation) ○​ There are MANY hypotheses on where and how organic molecules originated ​ Hypothesis 1: Reducing Atmosphere Hypothesis ​ Early earth atmosphere was highly active w/ lots of lightning, solar, and cosmic radiation as well as condensation, rain, gradient of temperature ○​ Lightning = source of energy containing molecules together ​ Top-down from lightning and sun to land ​ Hypothesis 2: Extraterrestrial Hypothesis ​ On meteorites - organic molecules formed interstellar clouds ​ Chemistry is happening and there are atoms everywhere in the universe. Asteroids and meteors were filled with chemical compounds and atoms, including nucleic acids. ​ Meteorites brought organic carbon to Earth, including amino acids and nucleic acid bases ​ Hypothesis 3: Deep Sea Vent Hypothesis ​ Underwater reactions with volcanic vents ​ Early earth was a giant ocean and the core of the earth was a highly active geological center inputting energy on to the surface of the earth ​ Bottom-up b/c lava, pockets of hot water and temperature gradient allowing for chemical reactions to occur ​ Biologically important molecules may have been formed in the temperature gradient between extremely hot vent water and cold ocean water  ​ ​ Overall, for organic molecules to form you need energy source, things to interact, and diversity of compounds for organic molecules to be formed ○​ Miller-Urey Experiment (1952) tested the reducing atmosphere hypothesis ​ They set up sterile anaerobic atmospheric conditions and electrical discharge, which resulted in spontaneous formation of simple organic molecules (monomers), which polymerized into simple carbohydrates, amino acids, and simple lipids ​ Basically energy from land strikes is creating these amino acids and organic molecules ​ To set up their experiment, they used gases such as methane, water (that they knew existed earlier) then they add electrodes to zap it all then water cools down the gas then they collected the precipitate (result) and they found that more chemical compounds existed than what they originally but in, just by zapping all the chemicals together with electricity, including amino acids. ​ (2) nucleotides and amino acids became polymerized to form DNA, RNA, and proteins ○​ Nucleotides and amino acids combined to form more elaborate compounds such as DNA, RNA, and proteins (compounds that have explicit functions and are useful). ○​ Polymerization = fusing of organic compounds ○​ Experimentally, prebiotic synthesis of polymers was thought impossible in aqueous solutions (because hydrolysis competes with polymerization and water loves breaking stuff down) → however, experiments have shown formation of nucleic acid polymers & polypeptides on clay surfaces from monomers to polymers ​ Clay acts as a catalyst/start to bring together these compounds to more elaborate compounds.  ​ Certain types of clay have a structure that can absorb organic molecules, meaning the molecules stick to the surface, concentrating and aligning them in ways that make polymerization more likely. Furthermore, clays have charged surfaces and metal ions that can catalyze chemical reactions making it easier for monomers (one nucleotide) to link up into polymers (linked nucleotides). There are no water molecules to break down the growing polymer chain. ​ (3) Polymers became enclosed in membranes ○​ Polymers such as DNA, RNA, and proteins need to be isolated in enclosed membranes in order to be activated and have an actual function, rather than floating around in the environment ○​ Polymers = fragile, easily degradable, can get hydrolyzed (water will break apart) and need to be protected from those harsh conditions. Hence, membranes and vesicles protect things from outside and inside environments. Hence protobionts explain the formation of a boundary that separated the internal polymers from the environment. ​ Protobiont (aka protocells) = ball w/ outside and inside environment ​ Aggregate of molecules and macromolecules that acquired a boundary such as a lipid bilayer, allowing it to maintain an internal chemical environment distinct from its surroundings ○​ Hydrophilic phosphate head and hydrophobic lipid tail ​ Protobiont = hypothesized prebiotic structure that represents an early step in the origin of life. It is like a non-living precursor to living cells that exhibit some properties that are essential for life such as compartmentalization and chemical activity. Surrounded by membrane-like structure (made of lipids) , the boundary separates the internal environment from the external environment, creating a defined inside, where chemical reactions can occur. Probionts show how non-living molecules could assemble into a structure capable of supporting life-long processes. ​ 4 characteristics that make protobionts possible precursors to living cells ○​ (1) boundary separated external environment from internal contents (boundary contained amino acids & enzymatic functions)  ○​ (2) polymers inside the protobiont contained information (DNA) ○​ (3) polymers inside the protobiont had enzymatic function ○​ (4) protobionts are capable of self-replication (inheritable and information being transferred) ○​ Living cells may have evolved from (1) coacervates (2) liposomes ​ (1) coacervates ​ droplets that form spontaneously from the association of charged polymers (like proteins, polysaccharides, etc) ​ Enzymes trapped inside can perform primitive metabolic functions ​ Formed in water without requiring a lipid bilayer and as no membrane - instead it has a diffuse boundary (selective semi-permeable membrane), where the internal environment can trap molecules allowing chemical reactions to occur ​ (2) liposomes ​ Vesicles surrounded by a lipid layer ​ Clay can catalyze formation of liposomes that grow and divide ​ Can enclose RNA ​ Highly stable & inside these balls, there an accumulation of chains of amino acids and RNA & formed when lipids are added to water ​ ​ (4) polymers enclosed in membranes acquired cellular properties ○​ Once the vesicles/membranes are formed, then, cellular properties like metabolism (synthesis of proteins) and cellular activities (reproduction, evolution, metabolism) ○​ Most scientists favor RNA as the first macromolecule of protobionts ​ Unlike other polymers, RNA has 3 key functions ​ (1) ability to store information: can generate proteins  ​ (2) capacity for self-replication: ​ (3) enzymatic function (ribozymes) ​ NOTE*** DNA and proteins don’t have all 3 functions RNA is highly versatile. Life doesn't use RNA to store information because it's ​ highly unstable due to its single stranded shape. However, it would be more stable if it had a double-stranded shape (DNA) ○​ Advantages of DNA/RNA/protein world ​ (1) information storage: DNA would have relieved RNA of informational role and allowed RNA to do other functions & DNA is less likely to suffer mutations ​ (2) metabolism and other cellular functions: proteins have greater catalytic potential and efficiency & can perform other tasks → cytoskeleton, transport, etc ​ Overall summary of the origins of life in order ○​ (1) formation and accumulation of organic molecules ○​ (2) polymerization of nucleic acids and proteins ○​ (3) formation of protobionts ○​ (4) synthesis of cell components by ribozymes ○​ (5) synthesis of proteins by DNA, RNA, and ribosomes ○​ (6) replication of DNA (helps create new cells and life) Lecture 3 (19) ​ The history of the Earth is divided into 4 periods ○​ (1) Archean ○​ (2) Proterozoic ○​ (3) Phanerozoic ○​ (4) Cenozoic ​ 3 types of rocks: ○​ (1) sedimentary ​ Sediments pile up, form layers, and become rock ​ These contain fossils ​ Igneous rock within/around sedimentary rock can be dated, providing age for sedimentary rock ○​ (2) igneous ​ Used to date rock layers because they contain radioactive isotopes, which are unstable, and decay with time (half-life). So, you measure  the amount of a given isotope as well as the amount of the decay product in an igneous rock ​ Igneous rocks are formed from the cooling and melting of molten rock (magma/lava). During this process, radioactive isotopes (unstable elements) are incorporated into the rock. Since these isotopes are unstable, they do through radioactive decay, transforming into a different element or isotope over time. The rate of decay of a radioactive isotope is predictable and is measured by its half-life (the time it takes for the isotopes in a sample to decay into its stable decay product. Then, scientists measure the amount of original radioactive isotope and new isotope (product of decay) to determine how many half-lives have passed since the rock formed. ​ Half-life = start 50-50, later 25-50, later 12.5-87.5 ○​ (3) metamorphic ​ Formed when existing rocks are changed by intense heat and pressure deep within the earth ​ Name factors that affect the completeness of the fossil record ​ Name factors that affect the completeness of the fossil record ​ (1) anatomy ​ Organisms w/ hard body parts (skeleton, thick shell, teeth) are more likely to be preserved than organisms composed of only soft tissue ​ (2) size ​ Fossil remains of larger organisms are more likely to be found than smaller organisms ​ (3) number ​ Species w/ larger populations or over a larger area are more likely to be preserved than those that existed in smaller numbers or smaller area ​ (4) environment ​ Marine animals or animals that lived near a water environment are more likely to become fossilized than land animals because sedimentary rocks are more likely to be formed in or near water ​ (5) time ​ Organisms that lived recently or existed for a long span of time are more likely to be fossilized than organisms that lived very long ago or for a short period of time ​ (6) geological processes  ​ Due to the chemistry of fossilization, certain organisms are more likely to be preserved than others ​ (7) paleontology ​ Certain types of fossils are more interesting to paleontologists ​ There is a significant bias regarding the locations where paleontologists search for fossils because they tend to search in regions where other fossils have already been found ​ Stromatolites: layered fossilized structures that are formed by the activity of microorganisms, primarily biofilms of prokaryotes (cyanobacteria). The biofilms trap and bind sedimentary grains or precipitate minerals, creating distinct layered formations ○​ Oldest known fossils on earth and they provide evidence of ancient cyanobacteria existing billions of year ago ○​ Hamelin Pool, Australia is where new cyanobacteria stromatolites are currently forming ​ Some pillars are 5 ft high and have taken thousands of years to grow ​ Geological time scale: ○​ precambrian = hadean & archaean (early, middle, late) & proterozoic ○​ Phanerozoic = paleozoic (cambrian, ordovician, silurian, devonian, carboniferous, and permian) & mesozoic (triassic, jurassic, cretaceous) & cenozoic (tertiary, quaternary) ○​ ​ (1) genetic changes and (2) environmental changes cause changes in living organisms ○​ Can allow for new types of organisms ○​ Responsible for many extinctions ​ Major environmental changes ○​ climate/temperature ○​ Atmosphere** ○​ Land masses ○​ Floods ○​ Glaciations ** ○​ Volcanic eruptions  ○​ Meteoric impacts** Lecture 4 (25) ​ Archaean period (part of precambrian) (3.8-2.5 billion years ago) (lasted 1.5 billion years) ○​ First cells = prokaryotic (lack nuclei) ​ Bacteria and archaea = similar, but have different metabolism/genetics ○​ All life forms were prokaryotic during the Archaean eon ○​ There was hardly any oxygen on early Earth, during this period, so organisms were anaerobic (do not require oxygen) ○​ We do not know if the first cells were heterotrophs ​ Heterotrophs = (humans) energy via consumption of food ​ Autotrophs = (apple tree) energy via production ​ Evolved as supply of organic molecules decreased ​ Autotrophic cyanobacteria were preserved, however their heterotrophic ancestors were not (stromatolites were evidence of life during this period) ○​ To be preserved they formed stromatolites, which are microbial mats of layered structure of calcium carbonate ​ They contain calcium carbonate because they are formed by the activity of cyanobacteria, which depletes CO2 in the surrounding water, causing calcium carbonate to precipitate ​ Proterozoic era (part of precambrian) (2.5 billion years ago - 543 million years ago) (lasted 1.9-2 billion years) ○​ About 1.5 billion years ago, during this era, multicellular eukaryotes (cells w/ nucleus) began to rise ○​ The first animals were invertebrates (cold-blooded, spineless organisms) ○​ Milestone in life = eukaryotes include all multicellular organisms / all eukaryotes = multicellular ○​ Bilateral symmetry facilitates locomotion, meaning it enhances efficient movement amongst organisms (body can be divided into mirror-image halves) ​ Beetle = bilateral, coral = radial, sponge = no symmetry ○​ There are 2 possible origins of eukaryotes ​ 1) individuals formed a colony and 2) single cells divide but stay stuck together  ○​ The consequence was that it allowed for complexity and specialization of cells ​ Volvocine green algae displays variations in the degree of multicellularity as there are species that range from unicellular to 8 cells to 128 cells to 2,000 (fully multicellular cells) ​ This displays evolutionary transitions b/c it shows how multicellular evolved from unicellular ancestors ○​ Modern eukaryotes have DNA in nucleus, mitochondria, and chloroplasts ​ Both archaea and bacteria contributed to the nuclear genome b/c there is evidence that eukaryotic cells evolved through archaea and bacteria; lineages b/c mitochondria has its own circular DNA and chloroplasts also have their own DNA apart from the nucleus ​ Hence, endosymbiotic relationships gave rise to eukaryotic cells ○​ Mitochondria and chloroplasts originated from a free-living bacteria that were engulfed by an ancestral archaea ​ This evolution occurred during the proterozoic eon ​ The phanerozoic eon had many phases which were separated by major extinction events → paleozoic (cambrian, ordovician, silurian, devonian, carboniferous, permian) mesozoic (triassic, jurassic, cretaceous), cenozoic (tertiary, quaternary) ​ The phanerozoic eon is when diversification of invertebrates and colonization of land plants and animals occurred ○​ Cambrian era (543-490 mya, lasted 53 million years) (marine animals, dramatic/abrupt life increase, first vertebrates arose) ​ It was warm and wet (no ice at poles) ​ Cambrian explosion → caused an abrupt/dramatic increase in diversity of animal species ​ The cause was unknown ​ Almost all modern marine invertebrate animals originated during this time as well as many others that no longer exist ​ Although new species have evolved since, there have been no major organizations of body plans and first vertebrates arose ​ Burgess shale = fossil place ​ Extinction event ○​ Odovician (490-443 mya, lasted 47 million yrs) ​ Diverse group of marine invertebrates including trilobites and brachiopods  ​ The first/ancient/primitive land plants and arthropods first invade land ​ Towards the end of this period, there was an abrupt climate change (large glaciers) resulting in mass extinction, where over 60% of marine invertebrates go extinct ○​ Silurian (443-417 mya, 26 mya) ​ Coral reefs appeared ​ There was a large colonization by terrestrial plants and animals ​ Spiders and centipedes ​ Earliest vascular plants → transport system for water and nutrients (xylem/phloem) ○​ Devonian = Age of fish (417-354 mya, lasted 63 million yrs) ​ Ferns, horsetails, and seed plants (gymnosperms aka flowerless plants), and insects emerge ​ Tetrapods (aka 4-legged animals) emerge such as amphibians ​ Near the end there was a prolonged series of extinctions that eliminated many marine species ○​ Carboniferous (354-290 mya, lasted 64 million years) ​ Rich coal deposits form ​ Coal deposits = sedimentary rock formations that contain coal ​ Very large trees, plants, amphibians became prevalent ​ Fern trees ​ The first flying insects arised ​ Amniotic eggs emerge, which are eggs that are protected by a membrane ​ Eggs used to be in wet environments only, but now eggs and animals can move to land (eg. turtle) and terrestrial land began to have more organisms ○​ Permian (290-248 mya, lasted 42 million years) ​ Pangea (a single supercontinent of all landmass) was formed due to continental drift ​ Amphibians were prevalent but reptiles became dominant ​ The first mammal-like reptiles appeared ​ At the end, the LARGEST known mass extinction occurred (aka Great Dying or Permian-triassic extinction) where 90-95% of all marine animals and a large amount of terrestrial species became extinct ​ This was caused by glaciations and or volcanic eruptions  ○​ Eruption resulted in fog and smoke which prevented plants to be able to perform photosynthesis and that caused all life linked to algae and plants to struggle ○​ Triassic = Age of Dinosaurs (248-206 mya, lasted 42 million years) ​ Reptiles were plentiful ​ First dinosaurs and first true mammals arose ​ Gymnosperms (non-flowering plants) are the dominant land plants ​ Volcanic eruptions led to global warming and mass extinctions ○​ Jurassic (206-144 mya, lasted 62 million years) ​ Gymnosperms were still the dominant land plants ​ Dinosaurs were the dominant land animals ​ The first known bird arose ​ Mammals were present but not prevalent ○​ Cretaceous (144-65 mya, lasted 79 million years) ​ Dinosaurs were still dominant on land ​ The earliest flowering plants (angiosperms) arised ​ Gymnosperms relied on wind pollution, however, angiosperms formed mutual relationships with pollinators (bees, butterflies, etc) and this drove rapid diversification ​ This ends with the most FAMOUS mass extinction (aka cretaceous-tertiary or K-T extinction) ​ A large meteorite hit modern-day Yucatan and this lifted massive amount of debris, which clouded the atmosphere resulting in an “impact winter” that lasted 2 years ○​ The climate change impact/cascade lasted roughly 10,000 years ○​ Tertiary = Age of mammals (65-1.8 mya, lasted 63 million years) ​ Mammals the survived the KT extinction diversified rapidly ​ Angiosperms (flowering plants) became the dominant land plant ​ Hominoids (apes, primates, etc) evolved about 7 mya ○​ Quaternary (1.8 mya - present) ​ Periodic ice ages cover much of europe and North America ​ Repeated cycles of glaciation ​ Certain hominids became more human-like ​ Homo-sapiens evolve 130,000 years ago ​ Summary of geological time scale:  ○​ The geological time scale was separated by formation and extinctions of species ​ Archean=bacteria and archaea ​ Proterzoic = eukaryotes ​ Phanerozoic ​ Paleozoic = land colonized ​ Mesozoic = dinosaurs ​ Cenozoic = hominoids Lecture 5 (38) ​ Evolution is defined as a heritable change in one or more characteristics of a population from one generation to the next ​ Microevolution vs macroevolution ○​ Microevolution = (small, gradual) changes in allele frequencies in a population over time ​ Population = all members of a species that live in the same area and have the opportunity to interbreed ​ Allele = 1 or 2 forms of the DNA sequence of a gene ​ Macroevolution = the formation of new species or groups of related species, which are broad patterns of evolution that happen over long periods of time ○​ Species = group of related organisms that share a distinctive form ​ What is a theory? ○​ Hypothesis = a question that is testable (falsifiable) and is based on limited evidence ○​ Theory = a comprehensive, well-supported explanation for a large body of information ​ Theory has predictive power, meaning it can generate testable predictions about future events or observations based on its established framework ​ Thinkers prior to darwin: ○​ Linnaeus = classified nature with a nested hierarchy (grouping organisms based on shared characteristics); binomial nomenclature (naming genus & species) ○​ Lamarck = adaptation to new environment & inheritance of acquired characteristics (are passed down to offspring) ​ Charles Darwin: his theory was influenced by geology, economics, and voyage of the beagle (voyage to collect plants and animals) ○​ Darwin’s influences/peers ​ Charles Lyell = geology → slow geological processes lead to substantial change & uniformitarianism hypothesis: time is required for recurring changes on Earth like erosion ​ This idea that earth was much older than 6,00 (very old) was important to Darwin ​ Thomas Malthus = economics → population growth is linked to resources ​ This idea was important to Darwin b/c only a fraction of any population will survive and reproduce when resources are limited ○​ HMS Beagle ship (voyage of the beagle) ​ The mission of the trip was to map the coastline of southern South America and Darwin’s job was to record everything (weather, animals, people, fossils, etc) ​ Importance of the trip to darwin ​ Darwin collected observations about plants/animals during the trip and he was struck by the distinctive traits of island species that provided them better use of their home environment (helping Darwin classify and figure more out about their environment) ○​ Eg. galapagos island finches → there are similarities in the species, but darwin noticed differences in feeding strategies ​ Specialization in feeding to obtain particular types of foods that differed among islands ○​ Formulation of theory: alfred wallace = darwin’s competitor and their papers were published together (darwin published origin of species 1859) ○​ Darwin’s evolution was based on: ​ (1) variation within a given species ​ Heritable traits (past from parents to offspring) ​ Genetic basis was unknown during this time ​ (2) natural selection ​ More offspring produced than can survive hence, there was a competition for limited resources  ○​ Traits that favor reproductive success (survival) became more common in a population ​ Contemporary evidence of evolutionary change → fossils, biogeography, convergent evolution, artificial selection, homology ○​ Fossils ​ Fossils display the steps leading to the evolution of tetrapods (fish to amphibian b/c fish and early amphibians have very similar features) ​ Even w/ an incomplete fossil record, evolutionary changes can be demonstrated ​ Fossils = transitional forms linking earlier and later forms/species ​ Horse morphology: ​ Horse fossil record has revealed adaptive evolutionary changes in size, foot anatomy, and tooth morphology (eg. horses used to be much smaller and looked less muscular) ○​ Evolution involves adaptation to changing environments and adaptations among organisms are produced from natural selection due to changing global climates ​ For example, horses used to live in forests where they couldn’t run fast due to so many trees, but later those forests were replaced with grasslands which allows horses to run fast (hence they’re currently fast runners) ​ Modern day horses = one-toed, but they used to be 3-toed and before that 4-toed ○​ Biogeography = the study of geographical distribution of extinct and living species ​ Isolated continents and island groups have evolved their own distinct plant and animal communities ​ Eg. southern california: the unique island fox evolved from mainland gray fox ​ During the last ice ages (16k-18k yrs ago), the bodies of water between the islands (channels) were frozen was colonized by grays fox ​ ○​ Convergent evolution = when 2 different species from different lineages show similar characteristics because they occupy similar environments  ​ Eg. anteater and echidna both have long snouts and tongues to allow them to feed on ants ○​ Artificial selection = programs and procedures designed to modify traits in domesticated species ​ Breeders choose the desirable phenotypes (observable characteristics like leg-length, size, hariness, etc) ​ Eg. dogs are bred to be fast and strong or simply looks cute ​ Eg. artificial experiment on corn happened when 163 ears of corn had 5% oil content, but they were bred to have high oil content (18%) and low oil content (1%) ○​ Homology (anatomical, developmental, molecular) ​ Anatomical homology = structural (bone/body plan) similarity between different organisms due to descent from a common ancestor ​ Eg. humans, turtles, bats, and whales all have “fingers” ​ Eg. same set of bones in the limbs of ^ tetrapod vertebrates has undergone evolutionary change to be used for many different purposes (walking, flying swimming) ​ Developmental homology = species that differ as adults bear striking similarities during embryonic stages ​ Eg. presence of gill ridges in human embryos indicates that humans evolved from an aquatic animal with gill slits ○​ Many animals in early embryonic phases look extremely similar to each; however during later part of being embryos, they begin looking different (although similar species embryo at later stage still looks similar eg. human, rabbit, cow & fish, salamander) ​ Molecular homology = DNA sequences of related species tend to be similar ​ similarities in cells at the molecular level indicate that living species evolved from a common ancestor or interrelated group of common ancestors ​ Eg. p53 proteins (that play a role in preventing cancer “guardian of genome”) and certain genes are found in a diverse array of (NUMEROUS) species ○​ Hence, sequences of closely related species tend to be more similar to each other molecularly than distantly related species  ​ Within the p53 protein, various diverse species have some amino acid sequence at the same spots; however closely related species such as humans and monkeys have more DNA sequences at the same location similar when compared to more different species such as humans and fishes Lecture 6 (35) ​ Molecular processes that underlie evolution = homologous genes, gene duplication, exon shuffling, horizontal gene transfer, genomic level changes ○​ Homologous genes = 2 genes derived from the same ancestral genes (but have evolved over time to perform similar or different functions in different species ​ Eg.the ancestral metal transporter gene gave rise to a gene that encodes a transport protein is responsible for the uptake of metal ions into the bacteria cells ​ Basically, a common ancestor has the ancestral metal transporter gene, then the common ancestor evolves into 2 distinct species and the copy of that gene was passed down generations to the new species, which also have the metal transporter gene. However, there was an accumulation of random mutations in the copy of that gene as it got passed down generations to the 2 new species. Hence, the exact DNA sequence of that gene is SLIGHTLY different. ○​ Genes duplication = rare duplication events that lead to the formation of gene families (groups of related genes that evolved from a single ancestral gene) ​ Paralogs are homologous genes within a single species ​ Example of paralog: globins (oxygen binding proteins) that are found in humans arose from many duplication events allowing for specialized functions ○​ There was an ancestral globin gene which duplicated multiple times and ended up forming different types of globins (hemoglobin, myoglobin)  ○​ Exon shuffling ​ Occurs when an exon (parts of genes that encode protein domains) and the flanking introns are inserted into a gene, producing a new genes that encodes a protein with an additional domain ​ Sometimes exons are duplicated or moved to a new gene then the recipient gene has an extra exon, allowing it to produce a protein with a new structure or function ○​ Creating new proteins w/ new abilities, leading to evolutionary innovation ○​ Horizontal gene transfer ​ Process when genetic material is transferred between different species rather than from parent to offspring (vertical gene transfer) ​ Can happen by a cell taking in free DNA from environment, viruses transfer genes between species, & bacteria transfer DNA directly through physical contain ○​ Genomic level changes = large-scale changes in chromosome structure and number, leading to the formation of new species over time ​ Eg. humans have 23 pairs of chromosomes, whereas apes have 24 pairs of chromosomes and this chromosome difference may have established hominids as a different species/lineage among apes ​ Genetic drift = random process that changes the frequency of a gene variant in a population (jar and marbles) ​ Population genetics = study of genes and genotypes in a population and its purpose is (1) to know extent of genetic variation, (2) why genetic variation exists, (3) how genetic variation is maintained (4) how genetic variation changes over the course of many generations ○​ Allele = a different/variant form of a gene; what is genetically inherited by each parent ​ Eg. eye color allele can be brown or blue depending on parent ​ Determines your genotype ○​ genotype = genetic makeup or hereditary information of an individual → composed of multiple alleles ​ Genetic code ​ What's inside ○​ Phenotype = physical appearance or observed traits in an individual due to genotype ​ What we see ​ Principles of inheritance = the way in which traits are passed from one generation to the next ​ Homozygous genotype = 2 identical alleles (AA or aa) ​ Heterozygous genotype = 2 different alleles (Aa) ​ Allele and genotype frequencies ○​ Population genetics is concerned with allele and genotype frequencies, which is a quantitative way to analyze genetic variation ​ Allele frequency = (# of copies of a specific allele in a population) / (total # of all alleles for a gene in a population) ​ Genotype frequency = (# of individuals with a particular genotype in a population) / (total # of individuals in a population) ​ To find allele frequency of the other allele after calculating one, just subtract the percentage/decimal/fraction from 1 ○​ Four o’clock flower (mirabilis jalapa) is a flower that open late afternoon/dusk for moth pollination at night and these flowers have many colors (white, red, pink, etc) (polychromatic) ​ Purpose of allele and genotype frequencies ○​ We calculate allele and genotype frequency to quantify the genetic variation in populations and knowing this data allows us to make predictions on what can happen to this variation, generation to generation ​ Tracking changes in allele frequencies across generations gives insight on population evolution (microevolution) ​ Hardy-Weinberg theorem ○​ models/predicts the expected allele and genotype frequency if they remain the same, generation after generation → this sameness is referred to as equilibrium ​ Equilibriums are the expected results if there is NO evolution occurring ○​ Equilibrium conditions = ​ (1) no new mutations occur ​ (2) the population is so large that allele frequencies do not change due to random sampling error ​ (3) no migration occur between different populations ​ (4) random mating ​ (5) no natural selection occurs  ​ If any of the equilibrium conditions does not occurs/is not observed, then we can say that the population is evolving (and is not in an allele frequency equilibrium) ○​ The Hardy-Weinberg equation: predicts the allele and genotype frequencies when a population is not evolving ​ p^2 + 2pq + q^2 = 1 ​ The point of this equation is to determine whether or not evolution is occurring ​ Where, p^2 = genotype of RR, 2pq = RW, q^2 = WW ​ If p = 0.7 and q = 0.3, then ○​ p^2 = 0.49 ○​ 2pq = 0.42 ○​ q^2 = 0.09 ○​ 0.49 + 0.42 + 0.09 = 1 ​ Microevolution: changes in allele frequencies from generation to generation ○​ These changes happen by (1) introduction of new genetic information or (2) mechanisms that alter the prevalence of alleles/genotypes ​ Natural selection = process in which individuals with certain heritable traits tend to survive and reproduce at higher rates than those without those traits ○​ Over time, natural selection results in adaptation ○​ Reproductive success = likelihood of an individual contributing fertile offspring to the next generation (fertile ppl) ​ Attributed to 2 categories of traits ​ (1) characteristics that make organisms better adapted to their environment and more likely to SURVIVE to reproductive age ○​ Eg. desert animals and arctic animals have different adaptations ​ (2) traits that are directly associated with reproduction ○​ Eg. brightly colored peacock males to increase reproductive success and mate ○​ Contemporary description of natural selection ​ (1) within a population, allelic variation arises from random mutations that cause differences in DNA sequences ​ (2) some alleles encode proteins that enhance an individual’s survival or reproductive capability compared to other members of the population  ​ (3) individuals with beneficial alleles are more likely to survive and contribute their apple to the gene pool of the next generation ​ (4) over the course of many generations, allele frequencies of many different genes may change through natural selection, thereby significantly altering the characteristics of a population ○​ Fitness = relative likelihood that a genotype will contribute to the gene pool of the next generation as compared with other genotypes ​ This is a measure of reproductive success Study Guide ​ Not tested on ○​ Species names ○​ Specific numbers (dates) ​ Things I need to know: ○​ Figures and pictures of organisms on slides ​ Be able to interpret figures or identify organisms in pictures ​ Important for lectures 3 & 4 ​ Images associated with each geological period (eg australopithecus, trilobites), or organisms involved in creating geological artifacts (eg. stromatolites) ○​ Key thinkers ​ Darwin ​ Lyell ​ Malthus ​ Linnaeus ​ Lamarck ​ Lectures 1, 2, & 3 ○​ Define myiasis and facultative myiasis ○​ What is sterile male technique (watch on posted yt video) ○​ EC question: What is the hidden curriculum at USF and every other large university? ​ Lectures 4, 5, & 6 ○​ Life definition ○​ Life’s minimal properties  ○​ 4 major overlapping stages in the origin of life ○​ What evidence do we have for each stage ○​ Memorize sequence of major events on earth ○​ Know the age of… (eg. age of fish) ○​ What animals went extinct when ○​ What is the K-T extinction and how was it caused? ○​ Definitions of ​ Macroevolution ​ Microevolution ​ Allele ​ Hypothesis ​ Theory ​ Convergent evolution ​ Homology ​ Paralogs ​ Genotype ​ Phenotype ​ Diploid species ​ homozygous/heterozygous ​ p53 proteins ​ Autotroph ​ Heterotroph ​ Anaerobic ​ Eukaryotes ​ Vascular plant ​ Radio isotope dating ​ Gene duplication ​ Horizontal gene transfer ○​ Not expected to calculate Hardy-Weinberg equation, but I need to know what it is used for, what it predicts, and how its elements (variable) are defined ○​ What is the contemporary evidence of evolutionary change? ○​ Describe the major molecular processes that generate genetic variation ○​ What is natural selection ○​ What is an adaptation ○​ How do you define reproductive success ○​ Know how to calculate allele frequencies ** do the Hardy-Weinberg questions provided on study guide