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Lectures 1-15 (Covers right after the first Midterm)

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Biology 3466B
Marc- Andre Lachance

Change in allele frequency evolution self-replication Frequencies allele evolution (some alleles are monomorphic, only have one allele in the whole population), the genes of interest are those that are polymorphic  For there to be differences in frequencies there has to be more than one allele  Mutation is the source of variation  The reason for different species is due to mutation  Fitness is the relationship between the genotype and environment  Common descent (the notion that we are related to monkeys)  Modification at molecular level (mutation), modification at higher level (splits into two, gradually changes over time)  Natural selection is the process by which natural selection chooses the experiments that work and those that do not  Prokaryotes in the 1920s o Cells have 2 genetic components, nucleus and mitochondria that have separate descent (prokarayotes), events like parasitism, sex, symbiosis, bound to happen once replication starts, not just changes in allele frequency, one cell swallowed another, failed to digest  Focus on the merger between genetics and evolution  By the time Darwin wrote the second, in the process of updating for the third edition of the Origin of Species, added a preface, eventually wrote 7 pages of acknowledgements Rebecca Stott, Darwin’s Ghosts, asks interesting questions, asked if Aristotle came up with evolution, if Matthews came up with Natural Selection as Darwin proposed it  Matthews wrote it in a footnote in a book about Timber  John Baptiste Lamarack (believed there was a smooth transition amongst people? Species?) o These relationships among species in the form of a family tree , extant species are on top of the tree (attributed to Darwin) o Lamarack though life was a continuum with minerals at the bottom, saw one string of progression from the least perfect to the most perfect (humancentric) , males the most perfect o The environment of the individual will have an impact, not only on the physical properties of the individual (giraffes have scarce resources, trying to eat leaves on top of trees, the principle of use and disuse kicks in, the necks become longer, somehow those properties influence the next generation o Pangenesis predicts that genes blend (if two parents are different, offspring look like a blend, granules blend) Darwin knew things could not blend, not a good mechanism to explain evolution o Lamarack put a lot of emphasis on the body could be changed by use and misuse, Darwin accepted this but didn’t sell it, thought it was a small contribution o Lamarack  environment directly changes the genetics of an individual (Canadian minister of science, we are involving every day, decade, walking on cement vs. Anything else, running shoes or high heels, we are involving in our environment, evolution is not individuals in our lifetime, it is a group over time, we are a slice in the evolutionary lifetime)populations reproduce over time o Invented the word biology, one of the best at the time of the French Revolution o Until much later (way after Lamark and Darwin, finally started understanding real genetics, epigenetics is now only being able to be proved) The selfish gene Richard Dawkins, the actual selection may be the gene itself, evodevo, what matters is not the genes, but when and where they are expressed during development, the only way to understand evolution is to break down and study one at a time Darwin’s cousin Galdin, performed blood transfusions on amimals, wanted to prove there were particles in the blood that could influence the genes, found no evidence at all Wiseman (German microscopist), took mice and cut tails repetedly, mate progeny, mated, no matter how much cutting, the mice always inherited complete tail, altering the body did not alter the genes, still didn’t know how genes worked  Wisemen instilled difference between germline and somatic cells (germplasm theory), image on page 4 , through time, germ cells give rise to more germ cells, in each individual, the somatic cells proliferate from the germ cell, they perform all function assicoated with plant and animal, don’t contribute to genetic info transmitted to next generation o Soma means body (don’t survive through time) o Can view bodies of vehicles of DNA (everything else that happens to bodies is fluff) o Natural selection is the all sufficient cause of evolution  Discovered nuclei contains chromosomes, these are able to divide  These ideas picked up by DeVries (given post of the credit, DeVries was the most notorious, the idea somatic different from reproductive cells), further determined inheritance of phenotypes follows precise patterns, he’s the one that came up with the term pangene and ‘gene”, figured out if you cross AAxaa, the first generation is heterozygous, the next will segregate, Mendel figured this out but no one knew (Mendel is 1860, Origin of Species, worked in a monestary, stopped being a scientist after)  Beijerinck wads the supervisor of x who was a PHD supervisor of Khuyen who was the PHD supervisor of Phajj (who was his PHD supervisor)  Conflict between people who thought mutation not selection was not the driving force of evolution  The dispute arrives from the discovery of genetics  Mendelians  DseVries, Bateon (invented terms like segregation, allele, heterozygous), Morgan (drosophila guy, didn’t like Darwin at all)  In 1909, Baeston published first textbook in genetics Monday, January 14, 2013-01-14 - Species don’t arise don’t arise spontaneously (Lamark) - Species decend from each other o We’re all related (common ancestor) o Darwin gave elements of how change occurs (Natural selection) th o Inspired by the writings of Malcus (wrote at the beginning of the 19 century) - Malcus looked at over population, interested in humans o Population growing exponentially o Resources growing linearly o Going to be a conflict between population and resources - Both Darwin and Wallace (published the idea of NS at the same time as Darwin), there are more offspring than the environment can absorb) o Individuals in a species differ in their characteristics (variation) o Some of that variation is heritable  Be careful with the use of the word heritable  Later we will use the term heritability very narrowly, not related to common descent o Therefore, there is a differential reproductive success in individuals in the population  Better variations (make them better adapted to the environment), will make them the one that survive  Whatever controls these characteristics that are beneficial will increase - Concept of Neo-Darwinian model  used and misused o Neo means new, meant to indicated Darwinism stripped off the problems Darwin had o Darwin didn’t understand how inheritance worked (was worked out by the geneticists)  Darwin used pangenesis, every part of the body contributed to transmitting information  Also believed in use and disuse played some role  Darwin was a little Lamarkian in his views - If you take Darwin and remove Lamark and Pangenesis, left with Neo-Darwinism - Mendel (paper came out approx 1860,for 40 years more or less ignored) o Devrise and Bateson started making the theory of modern genetics o The important part of genetics were large mutations  Discontinuous characteristics  Easy to study  Darwin focused on continuous characteristics 4 Schools of Thoughts that Historians Refer to 1) Neo-Lamarackism - Use and disuse - His book is on zoology where he explains his theory of evolutionary theory - Doesn’t really clarify what in his opinion drives evolution o Some kind of natural force, no clue of natural selection) o Over interpreted him, mostly philosophers, saw finalistic force o Evolution works towards perfection (goal), inherent impulse to become perfect called orthogenesis (ortho means correct or right) , there is no evidence that there is such a process - Inherent tendency of life elements to evolve towards perfection 2) Darwinists what drives evolution is natural selection 3) Biometriciansaccept natural selection, but bring in other factors - Say ancestry drives evolution, - Are statisticians - Very interested in humans, very racist in approach, interested in inequality of races o Differences in inequality of intelligence - Darwinists and Biomatricians are compatible, interested in continuous variation 4) Mendelians  interested in discrete traits (discontinuous variation) - Also were focused on mutation - There was a polarization - All schools of thought have tidbits of truth - Johannsen first element of reconciliation - Working with legumes (plants that had pods) - Wanted to know if length of pods had an inherited comparison o Used beans, selfed some beans for a few generations, made genetically homogeneous o Looked at distribution of length of pods o In a pure stock of beans, there was a distribution of length o Did that for several lineages, saw some lineages had higher mean and same variance o Found experimental evidence that the mean is inherited o Once you have a true breeding stock of beans, the next generation will have the same mean and comparable amount of variance - Attributed variance to the environment in pure stocks - Mean is a genetic component, the variance is the environment in pure stocks o When we look at the whole population with more genetic stocks, the mean is an aggregate of all other means, the variance is much greater  The variance component contains genetic information as well, is environmental and genetic (G+E) o In order to account for this, Johannsen coined the terms genotype and phenotype  Phenotype is the length of the bean, genotype is the inherited component  NOT what he said last week - Nilsson-Ehle studied the inheritance of colour in wheat seeds - Found that depending on the starting genotype, got different distribution of colour - Very interested in the segregation ratio of 15:1 o Started with red wheat x colourless (white) , have F1 that is pinkish o Dominance, not complete dominance) o Complete F2 by selfing the pink plants, end up with a continuum of colours o There were 15:1 of one degree of colour vs. No colour at all o Realized that this was a modification of 9:3:3:1 of Mendelian distribution, however 9+3+3 = 15 - Table on top of page 7 three different models o 3 loci, A, B, and C  Aa x Aa gives 3:1 ratio  AaBb x AaBb  AABB .... aabb (colourless) 15:1 ratio  AaBbCc x AaBbCc 63:1 ratio  RR RR RR x rr rr rr  get heterozygote at all three loci (Rr Rr Rr) 63:1, - Have the idea of incomplete dominance (intermediate dominance) - Characteristics controlled by multiple loci o Are additive between loci o Treat them as threex the same locus o If we have 3 loci, have one genotype that is RRR, will be really really darkly pigmented in red o If we cross with rrr, then we get a heterozygote at all three loci, will segregate 63:1 o Amongst the 63, have one that is very deeply coloured, then a bundle of distribution of the intermediates o Nothing magical about quantitative traits, explained using Mendellian genetics - Thought height controlled by multiple genes, eye colour - Goodrich wrote a book about the origin of living organisms, Mendelian genetics and Darwinian evolution fit together o Refer to the work of quantitative geneticists o Refer to naturalistic work, Melanic moths, found in proximity of birches, have a light form and dark form o Frequency of dark form change as a frequency of amount of industrial pollution o Thumpist after huge snowstorm found birds knocked down by storm, nurtured back to life, some made it some did not  Did statistical analysis of body size  Found in case of males, when bigger had bigger chance of surviving  For females, intermediate body size maximized survival  Data were all statistically significant (sufficiently large numbers) (page 7) Evolutionary synthesis - Evolutionary baseline unless we know what happens when there is no evolution, we can’t see what happens when there is evolution - Diploid means we need Mendellian ratios o Will be dominance o Convinced that dominance genes dominated o Dominant doesn’t meant that they “take over” o Doesn’t mean the population will be 3:1 o Is only 3:1 if you have 2 true breeding parents, cross, and then cross that generation - Can start with 100 parents with particular phenotype, 100 parents with another phenotype, don’t know what genotypes are, mate randomly, things become more complicated - Hardy worked on this problem with Punnet (page 8) o I should have expected the very simple point to be familiar with biologists (binomian distribution) o Weinberg had published it in such an obscure location that no one knew - Fischer demonstrated traits don’t blend, (F-test) o Invented most of the statistical tests that we did o Didn’t invent the student S test o Solve the problem Darwin had (thought traits blended during sexual reproduction) o If we follow Mendel’s model, the traits don’t blend  Wrote book called genetical theory of natural selection  Was a proponent of natural selection (Darwinian)  Sewall Writhgt was a proponent that the size of the population mattered o Small populations evolved faster, genetic drift (population error from sample size)  Haldane figure out the selective advantage of the moth - The equation came from Haldane o These three together laid genetic foundation to turn evolution into scientific model o Chomsky persecuted by Russian government, silenced by Licento (was a Lamarkian)  Fruit fly followed Darwinian and Mendellian model - Simpson worked with fossils - Stons - Took the work of Fischer, and popularized outside the circle - Stehpens worked with plants o Showed that it all fit evolutionary genetics  When all work done and published, became known as modern synthesis  most of the course known as modern synthesis 1942, Huxley family, evolution is not a stagnant thing, continued to evolve (page 9) o Epigenetics o When people come out with minor modifications, need to renew their grant, need Nature and Science papers, need to attract the best graduate students o Need to play the media game o Science is like any other human activity, corrupt, people will do things honest people don’t do, media stuff  Scientists have massive egos, one example was Kimura, in the 60s starting examining genetic variation in the 60s (how much variation is there?), when you look at animals and plants, not that much variation  There was a lot more evolution than expected  Neutral evolution Kimura most evolution at level of the gene is neutral, neither detrimental or beneficial, Darwin knew this was going to happen - Kimura was fairly modest, did blow the trumpet, this was a major challenge to Darwin, if you want to be famous, say Darwin was wrong - Everyone wants to prove Darwin wrong - I was an undergrad when that stuff was starting to come out  Steven J. Gold and his buddy Aldridge, formulated the theory of punctuated equilibrium, o Darwin said evolution was gradual  As natural selection selects for different things, genes change and phenotype changes o Based on fossil, Aldridge proposed that evolution happens through burst (page 9) o When speciation event takes place, considerable variation at speciation event, then variation becomes stagnant (time at y axis, phenotype on x, raise vertically after a while, little variation) o Modifying gradually the theory of evolution to account for new ideas in our methods o To complicate things even more, ideas such as that one get hijacked by people with alternate theories  Social Darwinism (let the rich become richer and the poor to become poorer, the people with more money are the ones that make the rules) o Darwinism as a term for anti-religion o The theme of the book is that Darwin inspired Hitler o Used and abused, continues to be used and abused o Hopefully by the end, have a rational idea of what evolution is about Monday, January-21-13 - When we look at fruit flies, all look the same - Rely on biochemical methods o Taking slats of startch, taking whole extract of individuals o Stain, to reveal the presence of enzyme activity o Become insoluble and coloured  Look at 2 situations where it is possible to find 3 bands on the gel  Have either 1 band or 2 bands per lane  There are 3 possibilities, but each individual can only contain 2 - Page 14 - How can an individual have 3 alleles (they can’t) o Can have one band or two bands but never three bands o WEBSITE o What could be going on here?  This is an allozyme situation  Can interpret the gel as a visualization of a single locus  This sample comes from a population where 3 alleles are present  Can have any combination of the three alleles  Means that the 3 alleles in question differ in how much electrical charge they have  The ones with the most charge move the fastest  The ones with intermediate charge move to the intermediate position  Co-dominant because we see both alleles with our eyes - First thing we do is count the number of homozygotes o 5 homozygous slow, 2 homozygous medium, 2 homozygous slow o 3 potential heterozygotes o Want to know whether these alleles are randomly distributed or if there is something interesting going on  Particular combination that is better  Natural selection favours those alleles In Figure 4 SS MM FF SM SF MF 5 2 2 2 2 2  pS = (10+2+2)/30= 0.5 o is the number of predicted the same as expected? 2 o predict (0.5) homozygotes o meaning approximately 7 homozygotes o 5 is a good approximation of 7 o Compare expected with observed  pM =  pF= - See whether this fits the prediction - Look at a situation where we either have 1 band or 3 bands - Many enzymes are multimeric o Means the gene codes for a particular protein, after translation monomers assemble and form a quaternary structure (maybe a dimer or a tetramer) - Multimeric- a structure composed of several identical or different subunits held together by weak bonds - First simple situation is SS - Other simple situation is FF - Finally, the only other alternative is heterozygous SF o Protein made by one allele made slowly o Protein made by the other allele moves fast o When you link together, make 2 slows together, 2 fasts together, and a slow and a fast stuck together (intermediate speed) o F= the square of its abundance o S= the square of its abundance o SF= 2SF (follows binomial distribution)  RFLPs – Restriction Fragment Length Polymorphisms (page 14) o Cut with restriction endonucleases o Recognize specific sequence o DNA gets cut into fragments o By electrophoreisis, if you stain the DNA, you get a smear  If you take DNA and cut randomly, the range of that size distribution is huge  When you purify genomic DNA, have millions of copies o Take, gel, blot on a membrane, take DNA, let it become single stranded  DNA will bind somewhere on the membrane where it complements  DNA that you put in solution will also have radioactive elements  Put it in the dark, develop the film, see where your DNA is  Get a piece of film, that band corresponds to where the piece of DNA of interest is  How much polymorphism there is at the level of the DNA itself  RAPID easy method o PCR based o Shouldn’t use it (worthless) o One instance where easy is bad  SSCP use in his lab o One easy way in which we characterize the population is by selectively amplifying one gene in many individuals o Pair of primers designed to amplify a particular segment o Want to find out how much variation there is in the population  Look for single nucleotide differences (SNPs)  Ran the DNA on the gel  If the gel has the right properties, will allow to recognize differences in the DNAs  Traces from 6 different individuals  Subtle differences  Small difference in band mobility can be explained by a single substitution  Look at different individuals in the same species, determine the SSCP, our hypothesis is that there are different sequences  Upon sequencing, find one has a G, one has an A o SSTP, take small piece of DNA, heat until it becomes single stranded  Stick on ice, DNA makes reannealing mistakes  Single strands fold upon themselves  Form hairpin loop structures  These structures are very sequence dependent (single strand conformation polymorphism), a different sequence won’t fold the same  Many labs use microsatellite typing (used by police to identify rapists, murderers), to establish paternity, do DNA fingerprinting o CODiS system (determine microsatellite patterns in humans) o There are splices along chromomes, special pieces of DNA outside genes (in spacer regions), are found in repeats (GT7) , at each end of the sequence is a unique piece of DNA  These regions are known as microsatellites  Repeats of 2, 3, or 4 bases  Bigger repeats called minisatellites  In telomeres, a lot of As and Ts o Repeats are characteristic for mistakes  Doesn’t take long for many repeat variants to arrive  CODis is 13 different microsatellite loci, find each have completely unique profile o See multiple bands because PCR is DNA replication in a test tube, generate error  Example 1 on page 14 o Females have slow allele and fast allele o Heterozygosity is the proportion of individuals that are heterozygous o Population can be monomorphic or polymorphic  Have 30 individuals, all identical o The last gel, one individual had a different band o If we search long enough, almost any gene will be polymorphic if we don’t have a special definition of polymorphic o Mutation is constantly acting on the whole genome at a low rate o Going to find polymorphism in practically every gene  Are these polymorphisms important?  Deleterious- remain at a low frequency  Neutral- may invade the population, may disappear  Is once in a million polymorphic? Never going to have homozygotes  P criteria, a locus is polymorphic if the most abundant allele<0.95) 0.95 max o Rare alleles are more than 5% abundant, chance that they may form homozygotes o Adopting the convention, if I want to decide if a locus is polymorphic, have to sample until I satisfy the criteria  Sample more until I am convinced the rare allele is less than 5% o More difficult to prove it is monoporphic than polymorphic (need to sample more to convince yourself H0is the right frequency) o A different criteria 0.99more relaxed as a criterion, may have reasons to do that)  Harris has published a lot on heterozygosity and polymorphism o Data used by Carvalli-Sfonza, studied human populations all over the world o Sickle-cell anemia o Example on page 15  Look at 10 human loci  Found 3 were polymorphic at the .95 level  Polymorphism in that population was 0.3  Does polymorphism fit better in the balance or classic school of selection?  Classic school Polymorphisms are transient (will either evade or disappear)  Balance school selection favours polymorphisms,  To measure heterozgosity, determine which alleles are heterozygous o One had heterozygotsity of 0.10, 0.51, and 0.39 o The other loci were monomorphic (unlikely to encounter any heterozygosity, assume it was 0 o Averages to 0.1 o 0.3 was the estimated polymorphism in that population  Consider 2 alternative situations o When studying the population at one locus, 3 different alleles o Measure their proportions, P2= P3 P1 P2 P 3 0.9 0.05 0.05 P11 0.81 P22 (0.05*0.05)= 0.0025 P33 0.0025 Heterozygosity = 1-0.81= 0.19 22 and 33are negligible P1 P2 P3 0.33 0.33 0.33 (1/9) (1/9) (1/9) 1-3/9 = 6/9 = 0.67  These two populations are polymorphic o Heterozygosity observed is 2/3 o The other population has very low heterozygosity o Polymorphism and heterozygosity are two ways of measuring genetic variation o Are two different things  Look at graph on page 16 taken by textbook, a plot of various kinds of living organisms, about the distribution of heterozygosity and polymorphism in different species o Mammals have lower heterozygosity and polymorphism than drosophila o Drosophila have a huge range o We if we find a line of best fit, find that some points lie above the line, others below the line  For these particular species, something is going on (for example, the range of drosophila is huge, the drosophila species that are going to far right away from the line of best fit have more heterozygosity than you would predict given the polymorphism o Maybe evolving faster? o Maybe balancing selection? o Less heterozygosity than predicted if below the line  Something is preventing heterozygosity  Maybe that species is better explained by the classical model Thursday, January-24-13 - HW equation made necessary b/c most orgasms studied are diploid o Is random assortment of alleles during meiosis o Need a baseline of allele composition (null model) - Is an advantage, that organisms are diploid o HW allow us to detect allele frequencies that are unexpected o E.g. if for some reason, in a population males and females have different allele frequencies, have an excess of heterozygotes  If the mechanism is always is always there, the excess of heterozygotes will always be there also  Sometime evolution means allele frequencies remain the same, however they deviate from the null model - When we are talking about alleles, talking about allele frequencies o p and q are frequencies o in drosophila, use + for the wild type o each group of geneticists have their own notation o something we have to live with  sometimes we can use P (proportion of the diploid)  p is the proportion of the haploid genotype - the equation is the expansion of the binomial distribution Aa x Aa A a AA Aa A aA Aa a - Punnetasquare tells us we have 2 parents, both are heterozygotes, at the time of meiosis, have ½ A gametes and ½ a gametes o That Punnet square allows us to do cross multiplication o Determine joint progeny of AA ,aa, and Aa o These are the same (genes don’t come in order), on 2 chromosomes o That’s why we get a 1:2:1 distribution o All the HW does is generalize this for other values of p  Interested in a population where p is not equal to 0.5  How can we expand this to make it applicable to any population?  Say p=1 (is a proportion, say q= 1-p)  Now, instead of 1:2:1, have (p)(p): 2(pq) : (q)(q)  Polymorphic doesn’t mean 2, it means more than 1 possibility - If we take this equation, represent every value of the 3 terms, vertical access is the frequency of diploid genotypes o Helps us appreciate different values of p and what effect this has on the potential to evolve o Evolution needs variation o This shows us how much variation there is o When p=1, no variation, every individual is AA - Heterozygosity is at a maximum when p= 0.5 (easy to pro
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