Bio200_first exam lectures
Bio200_first exam lectures BIO 200LLB - A
Popular in Evolutionary Biology
Popular in Biology
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Date Created: 06/07/15
BioZOO Evolutionary Biology What is evolution It s change through time Main lecture questions 1 How do organisms change 2 How do organisms across generation This is critical because It s not about change across generation rather about traits being moved by ancestors to their offspring Change within a generation is another field which is Ecology 3 What Factors cause these changes 4 How do organisms change through generation These two questions in specific Where do new species come from Why is there so many different species Different sort of organisms Few models aren t enough We need more variety 5 Adaptive Radiation ancestor s species have evolved many daughter species 6 Why do males and females act differently Look different In some male animal species they re flashy it s all about who s mating and who s not and how many offspring they have Example male sage gross a bird they have a lick breathing system the male come to a specific place called the lick and they sing and waggle their feathers and the females stand in a circle and watch the males and the best singer mates with all the females there The other males go home 7 why is there so many different types of penises in animals Why are there so many different looking flowers Basic questions help us understand the world around us 8 Agriculture evolutionary questions 1Food production 2Pesticide reduction 9 What is that governess attractiveness in both genders How do parental traits affect offspring success ls environment as important as genes End of lecture 1 BioZOO Evolutionary Biology Time scales History of earth We don t think of the Earth as entity Where did the earth come from and why is it perfect for life 1 The birth of the solar system was after the birth of our universe 2 Before the formation of our solar system a large rotating cloud of dust rocks and gas excised this cloud which is called profopanefary disk It contains Hydrogen and Helium That was produced during the big bang and more heavy elements that have been ejected by supernovas 3 46 billion years ago a star that was close to the protoplantary disk was destroyed in a supernova and the explosion sent a shock wave through the disk As the cloud from the shock wave began to accelerate most of the mass in the disk rocks dust and gas concentrated in the center of the disk they began to heat up because of the concentration of the mass at the center and that s the preformation of the sun most of it goes to the sun there s more left in the disk they remain to form the planet they re called early pieces or protoplanets 4 The heat in the center of the solar lead to the nuclear fusion for hydrogen and helium 2 Hydrogen s come together to make a helium Nuclear fusion eventually makes the sun Meanwhile Gravity causes matter to condense around those protoplanets that are outside the new of the sun gravitational grasp As this is happening the rest of the disk begins separating to rings that become orbits of our planet Larger fragments collide together and become larger and larger objects that become plants later These protoplanet 150 kilometers away from the sun it was the protoplanet earth 5 47 Billion years the earth was formed after the solar system 6 History of Earth It s divided to 3 periods unequal AKA how we divide time Precambrian supereon so long It s divided to 3 Eon s the first is The Hadean hell eon it s unified not so many changes no ocean no 02 no protective atmosphere Fully Molten filled with material leftover from forming the solar system In the end of the hadean era the earth surface cooled quick formed solid cross Earth went through a period of heavy asteroids new surface asteroids come down we get cracks steam escaped through those cracks and additional gases are released from volcano s from the core of the earth it continues to cool and clouds are formed form the steam rain is formed inside the clouds so we get oceans no 02 Volcanic activity was intense because no ozone layer ultra radiation flooding the earth surface By the end of the Precambrian superon the multicellularity aroused They were discovered by fossils But they didn t fossilize well because they had soft bodies BioZOO Evolutionary Biology The second two are themselves divided to Era s Paleozoic era 2 levels of decrease in terms of amount of time The appearance of soft fossils to the time where land was beginning to be dominated by large sophisticated reptiles and modem plants Example Archaeocyatha Mesozoic era 2 levels of decrease in terms amount of time Cenozoic era now 2 levels of decrease in terms amount of time History of the theory of evolution amp Mr Darwin 1 Supernatural VS scientific explanations for creation 2 History of evolutionary thought 3 Introducing Mr Darwin 4 Darwin s followers Most of us believe that all organisms were placed on earth by a divine power Came quick to believe that evolution shaped the organisms we re surrounded with What is it that prepared our world for a massive shift and how did Darwin present such a convincing case The truth is a lot of people built a foundation for his big idea The supreme being creates life and places it on earth They don t change immutable because if they change it means the creator wasn t correct divine powers People needed an explanation for super natural means 80 they started looking for answers beside divine powers Modern people started looking for alternatives too 16th Century BC Anaximander he wrote about his theory that all organisms came from common ancestors they had common descent transamination of new species that new species come from existing species Similar to Darwin s but long time ago Carlos s Linnaeus he proposed a classification scheme for life on earth was a member of a group of naturalist who understood the divine plan seeking rational organizations of organisms on earth Developed binomial nomenclature common genes species to give Latin names to organisms it limits the confusion of common names that species have People used multiple names for one species and vice versa He made the model Kingdom Order Family Genus These are critical because he did it on the divine plan god But the truth is that there were differences between species that are in the same genus don t look or behave similarly because of common descent James Hutton the founder of modern geology his ideas about earth as proper science examined rocks that earth Fossils are remains of animals from the flood Sedimentations were deposited by water and were compressed to form stone that s the definition He thinks sedimentations were slow that even the oldest rocks are made of materials furnished from the ruins of former continents The other reversed process occurs when rock is exposed to the atmosphere so it decays hit by rain and other elements that decays this coupling of destruction by eruptions and renewal by cementation He calls it BioZOO Evolutionary Biology the great geological cycle It had been completed numeral times and it takes centuries The earth is old He also proposed a system of gradualism in term of geological change profound change is the cumulative product of slow but continuous process Changes in rocks needs time He believes that geologic structures changed through time Adam Smith his book is called the wealth in nationals he describes the free market even though they thought its chaotic its not but it s guided to produce the right amount and variety of goods and services because of what he called an invisible hand he believed that with human motives were usually greed and selfishness that completion benefits the society as a whole by keeping prices low While still building goods for people He focuses on the importance of competition because it kept the market healthy that way Markets operate to benefit the business so people can make money not to serve community to win the competition Invisible hand but not supernatural keeping the economy health and growing as well as self interest even if its unconscious self interest Jean Lamarck he wrote the first truly theory of evolution He believes that super natural force placed organisms on earth and was driving up of what he called a latter of complexity Second environmental therefore natural force not a super natural force that adapted them to their local environment these use and disuse of certain traits that he believed would be past to future generations that means evolution He was associated with cartoons of Giraffes The giraffe wasn t born with this trait it acquired the trait Giraffe A has a short neck and spends life eating of short trees and her offspring are born with the same desire Giraffe B has a long neck and eats from tall tree s her children will have long necks Some Giraffes are born with longer necks so they re able to get more food and produce more offspring with long necks and pass it out to future generations You have to start with the trait not aquire it He was wrong about acquired traits BUT there s growing evidence that it does occur SOMETIMES Thomas Malthus he realized that population of people increase rapidly compared to the food supply available they grow geometrically but food supply grows linearly So when this happens competition happens Adam Why did it take time to be noticed He knows that society through history they experiences warsetc which limits the population Georges Cuvier he established comparative anatomy and paleontology by comparing living animals with fossils he analyzed skeleton remains of Indian and African elephants as well as mammoths fossils African and Indian elephants were different species and mammoths were either type of elephants he indicated that BioZOO Evolutionary Biology mammoths must be extinct that time it was wildly believed that no animal had ever become extinct because god creation was perfect No species of animal has ever became extinct Because god s creation is perfect He described a large Skelton he found and believed it s extinct he named it Megatherium represented another extinct animal by comparing its skull with living species of sloths He determines its a kind of giant ground willing sloth modern sloth The evidence of extinction suggested to him who was opponent of evolutionary thinking this evidence points out to him that there was a previous world where these extinct animals lived This world was destroyed by catastrophe the great flood from the bible Then the modern world came into being this theory is called catastrophism Charles Lyell who finalized James Hutton he s famous for an idea that past processes should be reflected in the present Present is the key to the past so he felt that geological remains from the past should be explained by geological process that are observable today this theory is called Uniformitarianism it states hat natural process operating in the past are the same operating in the present and are observable This means that it s the opposing view to Georges that says something changed our world that the past is unrecognizable to those in the present His interpretations of geological change as the study accumulation of new changes over long time was a powerful influence on Darwin its tons of tiny changes over time not a catatsrfy over time that is still going on to shape our world Robert and Darwin went on an voyage in a ship called HMS Beagle to observe boulders and report them to Lyell before the ship sets off Robert gave Darwin a book to read by his friend the first principles of geology he returns with observations and his own theories about formation of atolls that supported uniformitarianism so it takes long time to form His theory was correct Darwin and Lyell become friends Darwin who revolution the world with his theories of common descent and transmutation of species as well as potential natural selection as a biological change He met a famous natural historian to study with him his mentor recommends he surfs as a companion to Robert the captain so they were leaving on an expedition 5 years to continue their studies He found fossils of extinct mammals like a Glyptodont that contained seashells So he knew they were extinct recently no catastrophe mocking birds deferred in appearance depending on what island they came from He noted that local people can identify where a Galapagos looks like a turtle came from just by looking at it He believes that species must change through time When they got back to England an anthologist started looking through the bird collection and reported that the birds are actually 12 species Then modernly they added one more Darwin didn t take notes about which island they come from but other passengers took more notes Darwin realized that ancestors must ve arrived on these islands and BioZOO Evolutionary Biology become altered to form new species each suited for a different island 80 he began to study of the transmutation of species that new species come from existing species Alfred Wallace lives in a chain of islands between Asia and Australia he started collecting species and describing them then he moves to find out that all the islands he visited have similar birds He finds new birds between two islands Bali and Lamback there was an unseen boundary line that prevents the animals from moving across They must ve been at some while been connected He was correct The ocean is deep and these islands were never connected The line is called Wallace line He read the theory about the population while he was sick and bedded then when he was healed he started writing his theory and sends it to Darwin Darwin joined the work to his and published it Expanded by many people like 1 Gregor Mendel the first who understood the origin of genetic relationships the traits are inherited in a predictable fashion 2 James Watson and Francis Crick the ones who discovered the structure of DNA BioZOO Evolutionary Biology 0 Darwin didn t create the origin of life 0 Darwin big accomplishment was explaining the major force in creating new species from already existing species this is the idea of transmutation in species in common decent His theory centered a specific mechanism of evolution rather than where life came from Darwin has three critical pieces 1 There must be variation in the population 2 Variation must lead to differences among individuals in lifetime reproductive success 3 Variation must be transmitted to the next generation heritable If we have these three natural selection occurs 0 However for Ecologists who study natural selection in the present use these five criteria easy and testable questions Darwin s hvnothesis Five parts 1 Individuals vary 2 Populations tend to overbreed relative to available resources leading to a struggle access to these limited resources 3 Better variations must have better survival 4 Survivors will reproduce more than nonsurvivors wont 5 Traits leading to better survival and reproduction must be heritable Transmitted through generations Point 3 isn t necessary because survival could be low if reproduction is high enough in a short period of time We should be able to test each part and make predictions and see if natural selection can occur Darwin tried by these questions Do we see individual variation in natural populations BioZOO Evolutionary Biology Yes in shapes and color Do we see overbreeding leading to a struggle for survival in natural populations Yes but do all offspring who are born survive No in order to grow each of these seed links these need water nutrition and space Which means it s a competition with all the other plants in the area there s no enough room for oak trees and seed links Do better variations for a particular environment have higher survival rates Must be true to Darwin because any competition would lead to increase survival but it s complicated and is hard to know ahead of time which variation are better Even hard to know and measure the right thing Today we have dated directly variable that shows survival based on specific traits that are suited for changing environmental conditions Peter and Rosemary grant They worked on an island called Daphne Major they used natural selection to prove that Darwin was right 2 of the 13 species of finches they worked on lived on this island Medium ground finch and a large ground finch But the focus is on Medium Geospiza Fortis ground finches there s lots of natural variations in finches and beak sizes Most critical factor that lead to ground finch survival was seed availability most common food There was an extreme drought that leads to extreme decreasing in finches in one season Extreme population Unusually wet Abundant vegetation High concentration of small soft seeds Large hard seeds less common One of the surviving plants had large tuff seeds they re usually ignored So if we have two finches one will survive with the large beak so at the end of the year there will be long beaks survivors more the beaks increases by time and gets larger by size There was a wet season a huge abundant of seeds small seeds can fall off of large beaks High variation in survival smaller beaks flourish after this event and this is natural selection based on environmental pressure and does occur based on seed availability 1Do selected individuals have more offsprings than non selected Same question Do survivors have more offspring and pass on their selected traits to the next generation 2Do offspring share parental traits Darwin doesn t know but we do the same birds with large beaks their beaks changed during life so chewing these large seeds allowed them to acquire larger beaks BioZOO Evolutionary Biology Acquired traits are not heritable the bird who has bigger seeds and gets big beaks their children won t have big beaks While selected and survived individuals the offspring won t have the large beaks this is testable if it s acquired they won t be able to pass it in order to know we look at the offspring The grant tested it by plots they compared the parent to the offspring They found a correlation that they predicted the size which means its a heritable trait also the average increased during the drought Implications 1 Earth must be old enough for evolution to occur Hutton and Lyell both thought so and had increasing influence over he scientific and lay community and the depth of canyons and thickness of rock stara both indicated a very long and gradual natural process In the modern dating methods we know how old things are which had an increasing influence over the scientific and lay community 2 Fossils should show evidence of change through time Cuvier proved that they happen Organisms once existed Fossils continued to be found like Megafheriom Robert Own he examined these fossils and showed that they were close to live animals at that time This implication was supported even when Darwin was alive Fossils should show that species are mutable Two lines of evidence in Darwin s life 1 Older rocks strata should have fewer fossils of modern species than younger rocks strata Lyell showed the original data on Mollusks Most fossils found on the rock are modern species But super old only 3 is alive He gave evidence of implication 3 4 Gradual small changes through time indicate there should be intermediate forms in the fossil record 1 Are there fossils of intermediate forms 2 First fossil is found Know theses two species for the exam 1 Archaeopferyx is it a bird Or is it a reptile In between 2 Tikfaaik is a form between fish and amphibians a webbed end BioZOO Evolutionary Biology Darwin s evidence of evolution he had a lack of understanding of basic biological principle that we take for granted that s heredity It s a study of how traits are passed through generations he knew from observations of selective breeding where we breed live stock pets to influence certain traits He knew its because of that but not exactly how Physical resemblances from history people who worked in agriculture used breeding practices to enhance livestock for centuries but they didn t know how exactly resemblances came And people were to believe traits were blended But now we know that blending is a problem It doesn t work if all parents were to blend all individuals would have been identical Mendel began his experiments in plants on how traits are passed through generation Mendel did some experiments on plants they focused on how traits were passed He used the garden peas True breeders when they reproduce all the offspring look identical to the parents Flower color most peas were purple and some are white were two purple flowers were crossed pollen place it on the carpel only plants with purple came from the seeds that resulted This means that purple parents flowers breed true In some cases Parents that look alike give rise incongruous offspring These don t breed true and its not blending BioZOO Evolutionary Biology Once he had plants that true breeding purple he would cross one true breeding plant with a plant that bred true for a different variation of the trait he was focused on and this product is called a hybrid He bred the hybrids together to see if alternative forms of the trait can be observed the key thing he did was that he counted each offspring of each cross that had each trait Quantification of his results is what distinguished his work As well as his mathematical analysis that allowed him to see that traits would appear in predictable ratios 0 Simple crosses that he did between two individuals that defer in only single traits like Monohybrid mono means ones following the trait of purple flowers verses white the P parental generation is made when the true breeding parentsone purple one white to make hybrids they re said to cross fertilizecrossing the two types and the products of that cross is the F generation fellio means offspring In this case the product is all purple even though we had one of the parents white the second cross is called self cross and it is among individuals in the F1 because the pollen that is used to fertilize the carpel of the flower that it came from because plants have female and male parts the resulting self cross products are called F2 The monohybrid cross the outcome of the flowers purple to white ratio 31 so for every 4 seeds on average three will be purple and one white Mendel studied 7 traits in depths and all of them were 31 ratio He again self crossed the F2 to get an F3 generation and he found out that one third of the F2 is breed true 2 thirds don t breed true and the whites always breed true Each offspring we got from all the crosses showed one of the parental traits in tact in the F1 one of the traits is suppressed not expressed but that trait will reappear in the F2 generation the unexpressed trait is lightened trait its present but unseen 1 Mendel called each piece of information factors we call them genes 2 We know that copies of these factors come on separate chromosomes one copy comes in each parental gamy one chromosome from a moms egg and one copy of dads sperms or moms egg and dads pollen for plants 3 what do we call the alternative forms of Mendel s factors Alleles So when they re identical we call them homozygous for the trait homo means same when they re different heterozyote Hetro means different 5 in a heterozyote only one allele is expressed and this allele is called dominant the other one is recessive Dominant purple Recessive White Are these P generations Breed true No Is this P generation Heterozygote Yes because we have a white one A heterozygote can have offspring that expresses either dominant and recessive depends on the contribution from the other parent The alleles founded in an individual are called the genotype thus a homozygous dominant has a different genotype than a heterozygote The physical appearance of an individual is a phenotype the result of the expression genotype The phenotype dominant is the same as the heterozygote BioZOO Evolutionary Biology The 31 ratio is the phenotype ratio 3 purple 0 one white the genotypic ratio is one to two to one one homozygous dominant to two heterozygote to one homozygous recessive Mendel five elements have one main conclusion which is Mendel s first law of heredity or the principle of segregation The two parental alleles separate during gametes formation and are rejoined at random one of each parent during fertilization The results of this first law are made in a diagram called punnet square it s a way to symbolize a particular cross and then analyze By using this we can tell the ratio s that the cross will lead to Mendel question can we combine traits We know that F1 will be round and yellow and their genotype will be hydrozaygout and we call it a die hybrid or double heterozygote they show both traits no blending We cross them self cross once we segregate it Mendel had lots of data he increased the sample size the two traits appeared what we call assort independently we get all four combinations out of our dihybrid cross and if they didn t assort we would get wrinkled and green yellow and round Mendels second law of heredity is called the principle of independent assortment In dihybrid cross the alleles in each gene assort independently they go separately to different chromosome And we know that independent assortment is due to the behavior of individual chromosomes during gamete formation Choice of traits simple patterns of inheritance Mendel 6 of the traits were true He might have eliminated complicated ones Factors assorted dependently Each trait was controlled by one factor Factors did not interact Factors only had two alternative outcomes Factors were unaffected to the environment they were expressed in Those were all wrong First genes sometimes are linked sometimes certain traits almost always appear together because their alleles are linked It means when we cross 2 F1 3 we don t get all possible outcomes we only get the phenotypes of the parents Because the genes are on the same chromosome there s physical connection between alleles for two different genes Next Mendel believed all traits were controlled by single factors because his 7 factors were two state cases either or outcome white or purple most of the time the BioZOO Evolutionary Biology relationship between genotype and phenotype is complicated example Mendel traits for tall verses short plants In this case the tall plant were normal pea plants but the short ones had a single gene for a dwarf genotype so knowing this all tall peas are not exactly the same height it varies in different ranges it can be curved while dwarf verses non dwarfs is a two state case but height is not it s a continuously varying case it happens when there s more than one gene is effects one trait usually heights in most species l s called polygenetic inheritance The product of multiple genes interact to effect the phenotype of an individual this leads to more or less continuous gradation in the observe phenotype so some genes add height and some reduce it The more genes there s the more continuous the distribution The additive case of polygenetic inheritance differs from the non additive case this is another case where multiple genes effect the expression of a single trait and it s called apostasies we re talking about fewer genes Labradors coat color is determined by two genes that interact it s non additive because we don t know both genes we don t know the color of the dog Polygenetic inheritance if we knew any number of the genes we have some information about the resulting phenotype One of the genes is called E gene it determines weather dark pigment is present in the coat a dog with the genotype does not have pigment in the coat and has no dark fur so this is a yellow coded lab A Dog with a big EE or Ee has dark pigment chocolate and brown lab ee has no dark fur or a pigment We need one dominant The second gene the B gene controls how dark the fur is they have chocolate coats because bb has less intense of the pigment level BB black far higher pigment levels Mendel s factors controls single outcome but a lot of genes have multiple and unrelated effects the example is sickle cell anemia blood cells have sickle shape due to defect to hemoglobin inside the blood cells that s responsible for carrying oxygen The gene has another effect who have a single copy of this gene is undistinguishable its close to normal heterozygote for the sickle cell Are less to likely to get Malaria Mendel believed that there s two phenotype either dominant or recessive but it s not always the case two ways to know Incomplete dominance the off spring of the two homozygous is an intermediate form just like blending them Snap dragons a kind of flower when we cross them red with white we get pink Why don t all traits with incomplete domination have no variation The blending ends with the heterozygote when we cross pink flowers together we get red pink and white flowers so in this cross the phenotype and the genotype ratios are the same Type blood 0 have certain third alleles adds no sugar to the surface protein on the cell surface and it s homozygous to that allele Mendel only had genes with two allele types there can be more BioZOO Evolutionary Biology Mendel s garden where he grew the peas had different conditions soil stronger sunlight shading didn t effect the expression of his factors Darwin Darwin didn t understand how traits were passed on which is the principle of heredity Mendel s work on peas and extensions of his work clarified for us how traits are passed but he wasn t aware of the mechanics of heredity What keeps track of traits What is the physical mechanism of their transmission Understanding theses mechanism gives us support for the theory of evolution Mendel had no idea about genes and DNA or chromosomes aka factors genes at Darwins time BioZOO Evolutionary Biology Chromosomes were discovered in Mendel s time but they didn t know it can store heredity information traits When they knew that they come in pairs then the theory was suggested the pairing is central to the theory because its implied that each set of cells have a set of our father and another from our mother The number varies in different organisms Humans have 46 chromosomes one set of each of our parents 23 pairs from mom 23 pairs from dad each one of those chromosomes is comprised of coil DNA that contains hundreds of genes and other heredity information It determines our phenotypes for countless traits both physical and behavioral Cell division how chromosomes get passed on to produce gametes offspring they drive heredity information of traits Karyotypes it s a map made in a lab not the actual ones of a set of human chromosomes Homologous Terminology Once they condense and become visible after our chromosomes get thick before the replicate they re called Chromatid the DNA replicates and the two sister chromatids each have identical information their held tight with centromere then they re called chromosomes It s not an official chromosome until the chromatid replicates It happens to all chromosomes during cell division Two chromatid from dad and two from mom form a doubled pair 4 the same chromosome from mom and the same one with dad are called homologous pair Have same genes and information on them but different alleles Mitosis sister chromatid on an individual chromosome separate into different daughter cells one copy of each chromosome goes into each daughter cell In between cell division the DNA will start to condenses then replicate but its hard to see before this happens consist of two chromatid Metamic the structure that will pull the cell Meiosis 2 similar to mitosis once we got the daughter cells we have chromosomes lying then we get two daughter cells out of each at the end of the process each of them is a gamete A cell with a single copy of chromosome Hapliod 1N A cell with a pair copy of chromosome is Diploid 2N More than two copies is polyploidy XN One pair is dissimilar it s called sex chromosome Male chromosomes is tiny and little genetic information on them this pairing of different chromosomes where traits from the mother are displayed in her sons without any contributions from the father Crossing over beginning of the meiosis during this paring enzymes are released during these events the DNA from non sister chromatid are exchanged A Chromosome after crossing will have information with the mom The site and frequency in a particular chromosome is highly variable BioZOO Evolutionary Biology When we end meiosis we have 4 daughter cells that are haploid and likely to have different chromosomes This process which leads to high variation in offspring They keep mixing Gene linkage it occurs when we have 2 genes on the same chromosomes so alleles on the same one are more likely to pass together The F2 generation can produce 4 gamete combinations but its not always the case because the genes are on the same chromosome there s no way for a big A to pair with a b Genes that are close are tightly linked and the other ones is loosely linked If they re far they assort completely independently Wilhelm Johannsen the word gene Thomas Morgan genes rest on chromosomes From fruit flights George Beadle and Edward Tatum one gene codes for one enzyme Oswald Avery discovered that genes are made of DNA James Watson and Francis Crick published the structure of DNA and the means of inheriting DNA is comprised of intertwine two strains of nuclide They re referred to as double helix nuclide that form actual genetic code are fixed in place along in the back bones of repeating sugar in fore fight units by hydrogen bonds they effectively pair specific nuclides together They re held between together by hydrogen bonds they effectively holds them both Adenine A Thymine T Cytosine C Guanine G TA two hydrogen bonds CG three hydrogen bonds Why is it important that they re two strands because it suggest how genetic information is copied and passed on A single parental strand of DNA can give rise to two daughter cell the exact information as the parental strand Conservative replication the original parental strand is maintained in tact and separate daughter copy is generated Semi conservative replication a single chain from the parental is combined with a new chain to conduct two mix chains Dispersive replication mix of parental new chains throughout both daughtes DNA replication is semi conservative it insures continuity throughout the genetic code during all replication Because one old strand is always maintained It unzips parental chains by breaking the bonds and enzymes bring new nuclides and form the daughter strands DNA polymerase matching existing nuclides with new nuclides on the new complementary strands The central dogma The letters code DNA RNADProtein DNA is not only genes each of the genes codes for a protein or enzyme How do we get from genes nuclides to enzymes amino acids It s called the central dogma BioZOO Evolutionary Biology Portions of DNA s get converted to RNA s it provides instructions of protein goes and does the work of the cell DNA is the master instruction manual for the cell in order to do theses instructions copies of the nessairy portions are made Single stranded DNA strands they re called RNA copies they leave the nucleus to make other instructions to make proteins Then they go to the cell that needs protein Why is it important Because if RNA miscopies we have the original as a backup From DNA to RNA transcription From RNA to Protein Translation DNA does code for RNA to protein but a lot of genes that code to RNA doesn t end up as protein it works inside the cell Some genes can code to multiple protein depending on which genes are transcribed genes themselves are not the only devices of inherit transmission DNA encloses many proteins or other molecules which epic genetic markers they determine which portion is transcribed how often they re transcribed they pass through generations so changes in these proteins can change which traits are inherited Transcription for RNA always single stranded and DNA is single ONLY in replication RNA doesn t contain thymine but adds with Uracil similar to T to differentiate between the original and the copy separate role between DNA as information storage and RNA information transmission in the cell with A What is a protein Each gene is a series of instructions EVERY protein is made of Amino acids all proteins are different combinations of 20 amino acids Nuclides are ordered instructions for what amino acid comes next nuclide is grouped to three each three sum they re called code on And each code on codes for one of the 20 acids The universality of genetic is one of the strongest piece of evidence that all living organisms share a common evolutionary heritage When we sequence them we can see how many they ve changed Evolution BioZOO Evolutionary Biology Evolution means change through time But change in what Events that are occurring at the genetic level changes in allele frequencies what is an allele frequency Can we have it in an individual Yes frequency is interested in those that appear in a population a group of indivsuals we have the same set of genes but the allele is different Tongue rolling RR or Rr Inability to roll rr Proportion of rolling is 75 o for RR We represent it as a proportion of a whole How do allele frequencies change 1 Gene flow 2 Nonrandom mating 3 Geneticdrift 4 Mutation 5 Selection Process of how evolution works small changes frequencies micro changes that change through time Have the ability of frequencies Gene flow movement from one population to another What is the white allele frequency for white flowers 1 example in the paper Non random mating any allele has an equal chance of meeting up Mate assoraty bring similar alelles more often that expected because there phene same gene type assorted mating to cincreased in homozygotes Self feilizations can happen in plants Genetic drift causes changes in allele frequencies to due to small population size the founder effect The bottle effect Gene flow is allees moving from generation to another Genetic drift one population going to much smaller population Mutation don t change allele frequency at all the ultimate source to all new We won t have diversity without it variation comes from it BioZOO Evolutionary Biology Silent Mutations Framesth Point ts Mutations M39ssense Nonsense Sexual Selection Microevolutionary forces are a kind of evolution that doesn t match with Darwin s vision about evolution All the previous forces discussed were non adaptive forces they change allele frequencies but they may do so to benefit or the organism but it turns out that there s only one adaptive evolutionary force that is selection 0 Did the finches go through a bottleneck effect Yes Was it a genetic drift No What force changed the size of beaks Natural selection 0 All the microevolutionary forces will change allele frequency but non of them will do it in an adaptive way 0 What is adaptive A trait that is adaptive or adaptation allows an organism either to survive better or reproduce more The pollen that moved from the white flower to the yellow meadow didn t flow because yellow was better or more but because its more adaptive These forces may or may not cause adaptive change Adaptation is not the cause BUT for natural selection adaptation is the entire point 0 Factors required for natural selection to operate 1 There must be variation in the population 2 Variationmustleadto differences among individuals in lifetime reproductive success 3 Variationmustbetransmittedto the next generation Common selective forces BioZOO Evolutionary Biology 1 Predation 2 Climaticfactors 3 Parasitism 4 Mateattraction 5 Resourceacquisition There s one other type of selection Balancing selection 1 Heterozygote advantage 2Negative frequency dependent selection First we need variation to work on different phenotypes in the population Third these variations have to be heritable for natural selection to work Two variation must lead to differences among individuals in lifetime reproductive success there are many traits that are going to vary and there s many genetically controlled traits that are going to vary but only some of them will be adaptively advantageous These adaptive advantageous traits that allows their carries to have more offspring either directly increase production or they increase survival and therefore increase opportunity for reproduction as long as they re heritable the offspring will share these adaptive traits and there will be more of these well adapted offspring so it will spread the trait to increase the frequency in the population and all the individuals that have it will have more offspring that have it so we have more adaptive state Natural selection Example Species of mice that come in two color black and white Suddenly an environmental change happens makes it advantageous to have a black coat We start with black and white mice but the black mice had 3 times as many offspring from the white In three generations we have so much more black these black mice faired better than the white because they were naturally selected so the black mice will spread in the population Adaptation Natural change leads to a better production or survival but the only adaptation that are going to occur they re based on what s available from micro evolutionary forces These traits either already are present or a new come through mutations The option for adaption isn t endless What sort of environmental factors that lead to selection Predation is a strong selective force weather climates illness disease and food How you re going to find a mate And how to get food Example environmental pressure a predation as a selected force Some ancient lava flows in the south desert where the formation is dark rocks it s separated from sand whitest sand in the world separated of pale brown desert grass lings There s owls that eat these organisms like to eat all these organisms BioZOO Evolutionary Biology In the right area the white lizards and white mice in theses three areas is a strong selection Why is coat color is important in mice s dark mice would do better in pale places then white 30 when we talk about phenotype that are more advantageous to their carries its called fitness Organisms are traits that more likely be selected are said to have higher fitness than those who are not and fitness is quantified specifically the number of offspring that survive into the next generation Absolute fitness average number that reach the next generation Black mice 3 33 White mice 1 13 relative fitness Many phenotypes more than 2 it s called Relative fitness we note it as the ratio number of offspring to the highest possible offspring 30 black mice have the highest number possible of offspring White mice have a one of a highest total of 3 Several ways that selection can work selection can first act to decrease the variation in a population they do that in such individuals are closer to mean value to a particular trait stable selection get rid of variation when there s one virgin of a trait that works best for a particular trait We don t have a stable environment we get a different kind of selection which is called directional selection when the mean for a single traits is moved in one direction or another Disruptive selection where selection is there in both end in one trait selection against average trait value we see it when there s an environmental shift in a population in such two different phenotypes are successful Multiple phenotype can be selected but disruptive is not the only way we can maintain multiple phenotype by type of selection that is not that often discussed it s called balancing maintain multiple alleles or phenotypes in one generation in two ways 1Heterozygote advantage Anemia sickled cell in this case it has higher fitness lowered malaria sensitivity than either homozygotes both alleles will be maintained In the population by natural selection Relative finesses in Malaria areas AA75 Aa 1 Aa 25 2 negative frequency dependent selection the fitness of a genotype decreases as the fitness becomes higher rare individuals have a higher fitness common individuals have a lower fitness Rare individuals are more likely to reproduce So the rare phenotype is going to become more common common phenotype will be rare Sexual selection traits are selected because they attract better mates BioZOO Evolutionary Biology Elephant seals use their massive size roaring during the mating season 90 of male elephant seals die without having any offspring 10 can father 80100 off spring in a single season Darwin was the first to notice that each gender has a selected to check in the opposite sex like females don t mate with the first male they meet they compare and see who has more to offer they evaluate males don t do this Females are choosy because they invest 1Energyeggs they re huge defining features in females sperm the definition features in males 2time depending on it female bare the consciousness for a long time in other species a female is stuck with her choice before mating again The male needs time to convince another female to mate with him For male sex is cheap for female sex is extremely costy choosing the right mate is critical This difference is called parental investment This explains the difference between reproductively in females and males They do so by different ways like aggression displaying or both and colors What are females looking for 1 good genes 2 handicap principle Male show off characters handicap so there s survival and success 3 Runaway sexual selection females are not evaluating any currently relevant info instead they evaluate the ghost of selection past Long tales Male tales will be eaten before they can mate BioZOO Evolutionary Biology Products of evolution what s the point of evolution 0 How do species change allele frequencies Microevolution Over time we can get new species speciation is little micro changes to add up to big evolutionary moments called speciation What is it that makes a species No one can mistake squirrel and a barn swallow Or tree swallow and barn swallow even though they re closely related and similar Basic view on how we define different species by observing visible anatomical characteristics that differ between groups of organisms And this is how Linnaeus defined species in his theory referred to this sort of classifican based on anatomical differences as more physically observable traits Sometimes we can t differentiate between two species just by looking like Downey and hairy woodpeckers Closer inspection and mating call testing chemical instructions and DNA analysis visible or nonvisible we would find differences between them Even if we have trouble differentiating these species the individuals involved don t How do we differentiate then Ernst came up with the biological species concept defines species as groups of actual intro breeding national breeding which is isolated A species is composed of populations who s members mate and produce offspring or they would if they came in contact At the same time BSC indicates different species do not mate or cant produce fertile offspring thus they re reproductively isolated Plant species they hybridize all the time moving pollen even completely different species How is reproductive isolating is achieved Several mechanisms to prevent genetic exchange Two groups Before fertilization when the zygote is formed Prezaygotic isolating mechanisms prevent sex from occurring After forming the zygote Post zygote isolating mechanisms prevent the proper functioning of the zygote 4 types of prezygotic isolating mechanisms 1 temporal 2 behavioral 3 mechanical 4 gametic BioZOO Evolutionary Biology 5 Geographic or ecological isolation Individuals of one species must be able to breed important idea is to meet If we never go to the college same as the perfect mate we re not going to produce offspring its called proximity issue Geographically isolated like a river in between we won t be able to physically exchange genes they re called Allo Patric Allo other patric father of land Reproductively isolated Allopatric Sympatric same geographical land species that utilize different part of the environment rarely come in contact which causes breeding Lion male and female tiger can breed a liger can produce offspring but two ligers together they re infertile Tigon female lion and male tiger can t produce offspring Best ways to prevent breeding is for them not to meet The next mechanism temporal Species reproduce in different species or different times of the day These two plants one of them produces in the summer and the other in the spring so they can reproduce only in lab not in nature The third is behavioral mechanism Blue footed won t be attracted to the red foot because he s dancing wrong they only mate when the male the blue footed shows off the right way Why so many shapes of penises Reproductive isolation if you don t fit together you can t mate mechanical isolation We identify some species by their penises It s not always straight forward in some flowers in the proportion in the male and female parts in relation can limit a pollinator ability to transfer pollen to the wrong species Behavioral mechanism Physical difference prevents the transfer of gametes Last one Gametic isolation Chemical cues typically emanate from the egg fail to attract sperm or prevent from sperm from entering the egg common in species that directly relieas their gametes in the water nature They need to meet the wrong partner and not the wrong species Postzygotic isolation When two species cross the resulting will not develop Hybrid inviability the hybrid is not able to live However some hybrids survive in this case are usually infertile Example of this is Mule Liger survive but the offspring are infertile In later generations they re called hybrid breakdown All these isolations mechanisms exist between separate species most important to groups that are in process in separating species these are key in creating separate species BioZOO Evolutionary Biology Main reason we re studying geological and ecological ideas is because the simple idea gives us a clear sense how one species give rise to two in general it s all about isolation allopatric speciation An event that causes a separation of the original population into two different population with no gene flow between these two populations evolutionary process occurs separately in these two areas the population differentiate they become different genetically over time when we remove the barrier they re no longer able to produce offspring due to the isolation mechanism earlier discussed Most importantly we need separation and it be done in variety of ways 1 Dispersal small populations leaving large populations and starting new populations somewhere else where there s no fellow individuals Source of all species in the Galapagos 2 Vicariance isolation when a geographic barrier pops splitting populations into two like a river like the example moving of plates of the earth which led to oceans cycad ancient plants the distribution was confusing except they don t float which makes ocean crossing difficult 3 Missing link isolation Chain of separated populations they re close enough to move intermediate population go extinct the indivusals in the edge are so far that they can t transfer gametes effectively can isolate them Once isolation has happened no gene flow among the separate populations evolution is free to occur in the daughter populations and forces them to be on separate evolution Not just selection that causes reproductive isolation drifts is powerful assuming one or both of the daughter population is small random changes in allele frequencies in the new population can lead to new phenotype and behaviors that eventually isolate the new populations from each other slight change in mating or extreme change in phenotype Also Mutation can to Differential mutation like the frog can also play a role new mutation might spread in the population and push isolation from the ancestral population Which evolutionary forces prevents speciation Gene flow even small amount of genes counters isolation between daughter population It s huge to speciation events even very tiny amount of gene flow can stop the speciation process Can speciation ever occur in sympatric Yes check slides yes via polyploidy not common in plants check Slide It s not the only option for sympatric speciation disruptive selection can lead to speciation specially when combined mating in sympatric situations Two diverged phenotype selected for and these unlike individuals more likely to mate with like individuals either because they don t encounter indivusal or they have preferences for similar mates Then the population becomes seperated into two Same process in allopatric occurs in sympatry A lake small and homogenus can t divide them to allopatric portions there s 11 species closely related from outside the lake BioZOO Evolutionary Biology Sympatric speciation in Pea aphid plant eating insects in same geographic areas is found in two different plants they look identical but they show significant genetic differences highly ecologically specialized Pea aphids on alpapha lower fitness red clover lower fitness on that tree Same traits involved in the host but in different plants cause them to be reproductivly isolated 1 disruptive selection may occur some members evolved to feed on host Selection on different resoucrs 2 Observe sympatric speciation whole in the lab or field so its possible Idea of adaptive radiation when an organism enters a new environmental where there s underulized resources rapid speciation that leads to variety of species that make use of these resources when this environment have few species and volcanic change Hawaiian islands good for speciation because water barriers between the islands limits gene flow Not easy for species to move so encourages isolation They contain plants insects and snail species and birds Common tarweird given rise to the silverwords group of plants highly diverged with traits Speciation is progress the idea of a ring species incomplete speciation Different geographical areas have variable types of different phenotypes of species but can and do interbreed when they come in contact Local variance Sub speciation Evolutionary notation Describe evolution we use evolution trees or phylogenies to show evolution Through genetic history reflects Darwin s idea that organisms had common descent simple idea that one population can become two different species and these new two species are descended from a common ancestor Ancestral population is the shared of the two modern species it implies all organisms are related to each other with common ancestor Transmufafion of species one species becomes two new species come from existing species Firs example of the Phylogeny Dogs and Cats have More recently common ancestor than a common ancestor than maple trees Does this imply that a cat evolve from a dog Braches represent genetic change the further they move the more different the organisms are Nodes are ancestral species to all organisms that branch at that point 0 The split is ancestral event 0 Time runs from the past to Present 0 Tips are the species present in the current time organisms in the modern day they re all equally evolved and equally successful because they re alive they have adapted life in their own way all tips are considered successful 0 The most evolved is the oldest because it survived for a longer time Phylogencies are horizontal Time are vertical BioZOO Evolutionary Biology Organisms less evolved based on how complex to be common believe for many years called the great chain of being the lowest forms of perfection at the bottom organisms get closer to perfection like us vertical vision of life 0 Any tree the two organisms that most closely related are called the sister taxa groups of similar organisms we circle them and name them Mammals 0 Outgroup is the uncircled the one we are not interested in or is not involved in the sister taxa Maple Tree Most close one to the sister taxa Example on the slides The carpet moss is more closely related to the tree fern than to the volvox Because they share a recent common ancestor Twisting nodes means it s the same evolutionary relationships We can make sure by checking the sister taxas We want trees that show us how evolutionary history mutations tell us where bases diverge Parsimony 1 A preference for the least complication explanation for a particular phenomenon 2 A phylogeny that requires the fewest independent evolutionary events Traits other than DNA can give us information about relatedness Shared morphology Developmental patterns Behavioral patterns Paleontological data Traits that evolve through convergent evolution are called homplasious or analogous When a new form of an ancestral trait evolves it s called derived trait Shared traits that are passed on from a common ancestor are called homologous Look at the swim bladder in this picture Bi0200 Evolutionary Biology Fh tagmmt if tan is shared traits that are passed mm From if emmm a master if we sit LLEE i h m l g ans LEI151 rm 1 f a I39L J E Ill 39l quotPWv 1 l rm 3amp5 Ravi lent Harem clairElTis E im ttm arr when f3 new rm lm lamestmt trait Wattles it is anneal 393 d w d twist Homologous structure can look different but they re still the same same bones 0 When not using DNA we still can differentiate between homoplasies and homologous How does taxonomy relate to phylogeny Evolutionary relationships 0 Taxonomy doesn t equal to phylogeny
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