BIO120 Neat Notes PDF

BIO120 Neat Notes (All Lectures?) Lecture/Slide Deck 1; Intro into evolutionary Biology - The Theory of Evolution; - The theory of Evolution is the central unifying concept in biology - It essentially means that all living things have evolved fr...

BIO120 Neat Notes (All Lectures?) Lecture/Slide Deck 1; Intro into evolutionary Biology - The Theory of Evolution; - The theory of Evolution is the central unifying concept in biology - It essentially means that all living things have evolved from a single ancestor over 3.5 billion years ago - “Descent with modification” as said by Darwin is branching genealogy where each descendant is a bit different from the shared ancestor (like humans and chimpanzees who share a 6 million y/o ancestor) - As you go further back in time is harder to see how the major groups of animals, plants, microbes etc. are related, but you can see it clearly in their DNA - Evolution is a relatively new concept and a controversial one at that because it is in direct conflict with creationism which was and still is a very prevalent belief as to how life on this Earth came to be - The two core tenets of evolution are that - Living things change over time - Evolution is gradual and not instantaneous - It can take a small amount of time like years, or millions of years (an earthworm can't just evolve into an elephant) - Speciation (when members of a species split and develop their own characteristics) are accompanied by evolutionary changes and are greatly responsible for biodiversity and abundance of variation in plants - All known species share a common ancestor - Adaptations have arisen through natural selection - Natural selection contributes to the evolution of traits - Major areas of Evolutionary study - There are two main areas of evolutionary study; - Microevolution is evolution patterns/processes observed within a species - Macroevolution is processes and patterns observed among species - They both are interwoven and it's hard to look at one without looking at the other - Evolutionary history; - Focuses on the history of evolution and what was - Aims to determine evolutionary history of organisms (in terms of common ancestry) - Aims to identify and understand long-term patterns - Is more data-driven as you can't wait around 2 million years for evolutionary change to arise - Deals a lot with phylogenetic trees (uniparental genealogy which simplifies trees by taking info from only “one side of the family etc.” ) - Phylogenetic trees can convey same info and common ancestors even with nodes moved around and different sets of species - Evolutionary Mechanisms; - Looks to find the exact process responsible for evolutionary change - Identify major forces of evolution - Uses experimental and comparative studies of genetics and ecology, typically on the population level (not on individuals) (can construct experiments) - There are 4 main ways to study evolution - Comparative studies gather data from a large number of species and looks for patterns to emerge - Experimental studies manipulate systems to see what changes occur  - Theory helps to enrich understanding of things - Observational studies describe and quantify data given or collected - Relevance of evolution; - Childrens Questions; - Children are very curious and want to know more about everything like where we came from - Evolution can help explain that by saying we’re related to the great apes and older humanoid species like neanderthals - Medicine; - Looking at medicine through and evolutionary lens can help us see how new strains of disease (such as covid) mutate, spread and even predict evolution - It can help posit important questions as to how to combat illnesses and such - Agriculture; - Much of agriculture is plagued by weeds which are combated with herbicides - By applying herbicides we are applying selection to the weeds that are able to evolve and overcome the herbicides and survive - Agricultural evolutionary biologists look for ways to create more effect deterrents for weeds - They also look at the crops themselves to see how they are so productive and how to continue that trend - Environment; - Climate change applies selection to species and some will be able to evolve and survive and some will not - Biology; - Nothing in biology makes sense without the context of evolution  - Like mitochondrial DNA having a different genome than the nucleus through the theory of endosymbiosis (a proteobacterium enters a eukaryotic cell and its energy making abilities are used by the host to survive and the proteobacterium becomes an endosymbiont (cell living within a cell)) Keywords for this section; - Adaptation: (Noun) A trait that contributes to the fitness of an organism (improves its ability to mate and/or survive) (can be physical: eg. colour of wings | behavioural: e.g. attraction to certain smells) - (Verb) the evolutionary process that leads to the origin and maintenance of fitness increasing traits (an adaptation) - Biodiversity: The diversity of life on Earth/ number and kinds of living things in a particular area - Evolutionary History: A form of studying evolution focused on the history of evolutionary change, by data-driven studies looking for emerging patterns (works a lot with phylogenetic trees/uniparental genealogy) - Evolutionary Mechanism: A form of studying evolution that focuses on the mechanisms/processes by which evolution happens, through experimental/comparative means (typically at the population level) - Microevolution: Focuses on the processes and patterns of evolution within species (Micro has “i”’s so within which also has many “i”’s) - Macroevolution: Focuses on the processes and patterns of evolution among species (Macro has an “a” so among) Lecture/Slide Deck 2; Darwin's Big idea and how it Changed Biology - Before Darwin and Wallace; - People were questioning creationism and asking where are this diversity and adaptations were coming from - Argument from design - “Proof” of a creator posited by natural theologian William Paley - Payley wrote an essay about the argument of design; - Imagine you're walking along a desert and you come across a watch, you see that each part of the watch (The hands, the strap, the gears etc.) serves a purpose, each part is functional, it was made with a design and a function in mind - so you can conclude that somewhere on Earth there is a watchmaker (who made this watch with a clear function in mind) - Now imagine you see a rock, you can't really find any purpose for a rock, that the face is good for eagles to sit on or to block a path or some such, it's just a rock, maybe different from other rocks but not in any significant or deliberate way, it doesn't have a function and so it doesnt need to have had a designer, it could have just arisen from natural processes - But look at a joshua tree, the tree is waxily coated, desiccation resistant, have silica and barbs that are herbivore proof and chlorophyll for light/energy absorption, all these things are incredibly complex and specifically designed with a purpose and function in mind, so it must have had a mind behind them to make it, a divine designer - Dominant thinking in Darwin's time and he studied natural theology as well - Jean-Baptiste de Lamarck - Darwin was not the first to propose evolution, before him there was Jean Baptiste de Lamarck who had a theory for evolution but was later proven to be wrong - He was the first to posit a mechanism of evolution (and use the word) - the inheritance of acquired characteristics; - Imagine a giraffe on an african savannah - It east leaves and can reach the low leaves but the high leaves are just out of reach so it will spend its entire life trying to get to those leaves and through this repeated exercise it will acquire a longer neck which is can then pass down onto its offspring - That organisms can alter their phenotype through exercise and then pass this change down to future generations - That changes in somatic cells could be passed down through germ cells - There was hierarchical pov in the world where everything was created by the creator from very simple organisms to very complex ones - Lamarck posited that all life starts out very simple then through the acquired characteristics it becomes very complex, and once we run our of complex organisms, the creator makes more simple ones and that explains the diversity of evolution and simple/complex organisms - Lamarck was proven wrong by August Weissmans germplasm theory (1889) - That germ cells (gametes/sex cells) are the agents of hereditary and that somatic (body) cells cannot pass down hereditary information - That genetic information flows in one direction from DNA to proteins (from gametes to somatic cells) - He cut off the tails of a bunch of rats then bred them and the offspring all had intact tails which proved lamarck wrong - Darwin and Wallace and the development of their idea - Darwin “first” came up with the idea of evolution but also independently Alfred Russel Wallace had discovered it and corresponded with Darwin to discuss it (they both independently discovered natural selection which is the chief mechanism of evolution) - There are two major points to the theory of evolution - That all living things are descended from a common ancestor with modification over time - Natural selection leads to evolution by operation variation on individuals - Darwin - Was born into a rich family full of socialists and a doctor father who wanted him to become a clergyman or doctor when he grew up - Dad sent him to university of edinburgh to study medicine but darwin hated med school and the dissections and whatnot, had mediocre grades - Exploration was a big part of what made Darwin Darwin - He went on the HMS Beagle (map making expedition) as a naturalist (position made for him because captain wanted someone of noble class on the ship) because his teacher noted he loved nature - He made collections that went to museums and numerous observations - Upon his return he went into seclusion for the rest of his life to sort through all that he had seen and discovered - The second thing that catalysed his discover on ThoE was reading Chares lylle’s book “Principles of geology” which argued for uniformitarianism - That the processes that formed the earth today are the same as the one ones that formed the earth in the past  - That the world is not static and erosion, earthquakes, volcanoes etc, formed the earth to how it is, always has and always will - That natural processes are the same today as they were in the past and that they will be in the future - Darwin took this to mean there exists a dynamic world that has changed build up gradually today, same as the past - On his voyages on the Beagle he had a keen eye for differences in individuals in populations (like humans in a room) and slight differences in populations in different places - He noticed 4 different types of mockingbird on 4 different galapagos islands and wondered why the creator wouldn't just put fully different birds on each island, why the same bird but slightly different (this led him to think they all got to the islands the same and then changed) - When he got back he read Thomas Malthus’s ‘An Essay on the Principle of Population’ which basically said that without limits population should grow exponential but resources dont so there must be some individuals in the population that dont succeed to survive (important contribution to natural selection theory - He then posited that favourable variations would be preserved - At the same time that Darwin is thinking about all this, Russel has also read Malthus and is also thinking along the same liens that the best hunters, best digestion etc. will survive - He mails Darwin who gets scared because he wrote that same thing a decade ago but chicken out, lyell suggested  they propose their theory together and they did to the linnean society and it didn't make waves - But when Darwin published his book (year later) it sold out and made a huge impact on the public - Mechanism of Natural Selection - THIS IS A VERY IMPORTANT CONCEPT - Natural selection needs to have three things - Variation, individuals must vary in a population - Hereditary, the variations must be heritable - Differential fitness, some must have higher fitness than - VHD - Darwinian Evolution: A revolutionary new model - Lamarck vs darwin - In lamarck’s model (Transformational evolution) ; - organisms are born, acquire traits over their lifetime (straight line) then pass that to the next generation (dashed line) - they all have an equal chance of leaving behind offspring - In darwin's model (variational evolution) - Organisms don't undergo significant evolutionary changes/adaptation over their lifetime but the population does see a change in the frequency of who leaves offspring behind - Not everyone in this model has an equal chance of leaving behind offspring - Important elements of Darwin's ThoE - Evolution occurs at the population level  - Variation is not directed by the environment (people can't develop adaptation when needed) - The most “fit” depends on the environment - Evolution works with available variation and may not achieve perfection (has to work with variation that present, cant cause variation) - Implications/Applications of evolution - As we apply antibiotics to a bacterium we are applying selection to the bacteria to develop antibiotic resistance - Anti bacterium that has developed a mutation that allows it to be more resistant will be favoured in the next generation and be more fit than its relatives - There is no forethought to evolution - Even before we apply antibiotics some bacteria are going to be resistant and they will leave behind more descendants Keywords for this section; - Uniformitarianism: Natural processes today behaves as they did in the past and will continue to behave so in the future - Natural selection: A mechanism of evolution that is caused by variability of individuals to leave offspring in the next generation (higher fitness = more offspring) - Evolution: The change in (the proportion of individuals) with (certain) heritable traits over generations - Mutation: Change the DNA sequence of a cell (transmittable from parent to offspring)  - Genetic Drift: The change in frequency of a certain trait in the population due to random chance - Antibiotic resistance: the ability of bacteria to be resistant to certain medication designed to eradicate it Lecture/Slide Deck 3; The Evidence for evolution - Darwin's Beagle Voyage; - Aged 22 darwin was the ship's naturalist which was on a map making trip in south america - There he made numerous observations of follis, flora, fauna, oceanic islands and the geographical distribution of plants and animals - As naturalist he was primarily responsible for making observations of nature - Evidence from Geology - The Beagle touched down in argentina after brazil (where darwin found no fossils) - When in argentina he found fossils of these huge armadillos which had not been seen alive in argentina or anywhere before, but resembled modern (smaller) armadillos - From this he starts to think of them as related and bounces around the thought of how species can change over time - He continued to collect many fossils for study - Modern Paleontology; - The tiktaalik “fishapod” was discovered in 2006 on ellesmere island in nunavut and - It's a tetrapod (four limbed animal) (we are a part of the clade) - Predicted by evolutionary biologists because of rich fossil record of tetrapods - There was no proof of the intermediate step from limbed fish to tetrapods before the tiktaalik which had these intermediate features  - It sits between tetrapods and fish in a phylogenetic tree because it has crude tetrapodal features (like the forelimbs) but still is in water and not very much on land - Looking at the evolutionary history of whales; - People knew they were mammals early on but who are they most closely related to morphologically - An expedition in pakistan and central asia helped fill in these gaps with fossils which show that their closest relative ar ungulates (hooved mammals likes cows and hippos” - Fossils show very early forms of whales that are on their way to modern whales with elongated snouts, longer bodies and reduced limbs (some have been reduced completely) - You can still see hind limbs in some whales (like belugas) which are vestigial traits - Basically; - A very old earth allows for lots of time for evolution - Fossils provide proof of intermediate forms between seemingly unrelated species (whales and ungulates, tetrapods and fish) - More recently preserved fossils resemble modern species more than older preserved fossils (which show more differences from modern species - Evidence from Homology - Darwin's famous galapagos discoveries - Homology is similarity of traits between organisms due to a shared ancestry - Mainland Cormorants; - Semi-aquatic diving birds that do not have the best waterproofed feathers - After diving/getting wet they will perch in trees and spread their wings to dry them off which is a very taxing activity  - They are strong fliers and have use of their wings - Galapagos cormorants; - It's a much different topography with little tall vegetation and its very dry - So there cormorants prefer to nest in the ground and have a short little hop to the ocean for fishing and food - Because they didn't need to fly these wings became vestigial - Vestigial structures arise when a trait is not used for many generations and mutates to become non-functional - Vestigial structures are morphologically and functionally reduced structures inherited from an ancestor - Evolution favours changes that reduce the cost to live, like removing useful eyes from fishes that live deep in the ocean where there is no light - Humans have ear muscles (move towards threats), appendix (was important for digestion), tailbone (most primates have tails), goosebumps (for looking bigger with fur and keeping warm with fur) - Not all homologous traits are vestigial - Like looking at the forelimbs of many tetrapods you see that they share radii, ulnae, metacarpals etc. even though they might not make the most sense to keep evolutionarily - There is also homology in genetics, there are about 500 shared genes across all life, no matter how distantly related - Basically: - Vestigial traits provide evidence of evolutionary past because; - The have reduced to no function in modern organisms - Can only be explain by a functional trait in an ancestor - Homologous traits are the same across organisms;  - Similarities which prove common ancestry - The structures have evolved to have vastly different functions - Evidence from Biogeography - Going back to the Galapagos’ - Its made up of 15 relatively young volcanic islands that contain flora and fauna that colonised from mainland south america - Darwin in the galapagos - A very dry, cactus-full and rock sharp unwelcoming island - Evidence from colonisation patterns; - He noticed cacti that looked incredibly familiar to the cacti he had seen in peru just a few weeks ago and began to think about how those cacti could have made it there - The cacti have really juicy fruit that birds love, so the birds must have eaten the fruit and gotten blown off course of migration and bird poop with the seeds over millions of years the cacti established a population there - He spent 5 weeks in the galapagos and noticed only taxa that would be good colonisers, meaning their ancestors could have survived the journey over salt water, unlike freshwater fish and amphibians - Highly filtered biota = mainland origin - Patterns of variation; - He noticed varying tortoise types on varying islands - The ones in more humid islands were bigger with shorter necks for ground vegetation but ones on drier more volcanic island were smaller with longer neck from eating cacti - This pulled lyell’s thinking (uniformitarianism) into his mind about how the same animals put apart  with slightly different circumstance s will be slightly different - Darwin's Finches; - Darwin noticed there's finches on the galapagos and took specimens back to england think they were all different species - An ornithologist friend of his told him they were all the same bird - Darwin the posited that a finch must have gotten there and had the opportunity to branch out millions of years ago - Australia; - Is a very isolated land mass with very distinct flora and fauna - Has high endemism meaning that lots of species are found there and not elsewhere - High biological uniqueness due to isolation - Mammal pollinated plants could have arisen from an ancestral plant that got there but its insect pollinator never made it, causing it to evolve pollination mutualism with small marsupials - Marsupials in australia fill the role that placental mammals fill everywhere else, like there are marsupial counterparts to common placental anteaters in south america - This could mean that only a marsupial ancestor made it to australia and filled those roles - Biogeography since darwin; - Geographically close organisms tend to resemble one another because daughter species tend to be concentrated in the same geographic areas - Different groups of organisms in similar climates in different parts of the world can lead to evolutionary  convergence where they evolve similar traits typically to combat similar issues despite being distantly related - Lessons from biogeography; - Remote island biotas; - Are dominated by good colonists that are related to continental counterparts that evolved to better survive locally - Biogeographical isolate regions; - Have species adapted to niches unusual for their group and harbour endemic radiations that are convergent with radiation elsewhere - Basically meaning that species have adapted to conditions unusual for their group and are endemic with similar counterparts elsewhere - Evidence from Domestication - After the beagle trip he comes back to england, gets married and lives out the rest of his days at down house - He has a large amount of info to sift through and beings to play around in his garden - Breeding plants and imposing artificial selection trying to understand how all the biological variation he saw may have arisen - He begins to think more and more about selection and how that can be the key to evolutionary changes and that's what people do when they are breeding crops or purebred dogs for certain desirable traits - Like teosinte and corn which are very phenotypically different and can interbreed like dogs can (interfertile) - Artificial selection can be very powerful like a french bulldog being more closely related to a wolf (direct ancestor) than a coyote - And pigeon fanciers who through artificial selection can make really weird looking pigeons  - “Artificial selection can be just as powerful an agent of change are whatever generates diversity in the wild” - Vast amounts of heritable variation found within species means that that this variation can be acted upon to produce desirable traits which is only possible if there is already a lot of variation in the population - Artificial selection is the human imposed version of natural selection (darwin use art selec. To make case fro nat selec.) - Evidence 165 years on - Antibiotic resistance, herbicide reistanct, adaptation to pollution,e xperimental evolution are all proof of evolution in action - The speed and strength of natural can be much faster than darwin ralsied like breeding corn form teosinte in just a few dozen or hundreds of generations - DNA evidence for vestigials and homologous trais which show molecular evolution - Fossils strengthening the evidence of the tree of life Keywords for this section; - Endemism/Endimeic: Species occurring in one place but not others - Vestigial: Remnants of a once useful biological stucture in a species stemming from a common ancestor - Homologus: The similarities in species due to a common ancestor - Marsupials vs Placental: Masrupials raise newborns in pouch while placental rgowins in mother till birth Lecture/Slide Deck 4; The evolutionary significance of genetic variation - Intro; - Will talk about where genetic variation comes from, how its inherited and how it influences trait variation - VHD as a mechanism for natural selection - heritable variation leading to differential fitnes  - Heritable variation is largely genetics based - Variation is everywhere around us, even in pigeons and you can observe various phenotypes everywhere - Sources of genetic variation; - Mutations; - Mutations are stable (failed to get caught during DNA proofreading) changes in the DNA sequence arising during replication in meiosis and mitosis - Can be different types of mutations which we will cover later but basically when there is a mistake in replication the replicated strand will replicate and give rise to a mutant strand of DNA that can have the following possible effects on fitness (if occurring in a germline cell); - Neutral; - The mutation doesnt matter - Deleterious; - which has a negative effect from weakly harmful to lethal - Benefical; - Its very rare for there to be a beneficial mutation/have a positive effect on fitness - Mutations are quite rare because they tend to be corrected by the DNA Proofreading but sometimes mistake happen and they slip through the cracks - Charcteristics of mutations; - Mutation is inevitable an no life on earth has a 100% DNA proofreading mechanism to have perfect DNA replication - Mutation is not directed; - You cant wish for a mutation to happen, they are isolated and just happen - The mutations you get have nothing to do with if they are good or bad - Rates of mutation vary;  - Certain parts of genome are more likely to accumulate mutations than other - Environment has an effect on mutations; - Higher temps can lead to lower accuracy replication - Organisms exposed to mutagens can have wild (lol) DNA and higher rates of mutations, but higher mutation rates has no effect on type of mutation (deletriour, beneficial, neutral) - Types of mutations; - Point mutations; - When a single base pair is added, deleted or changed at a point - ATGCAGT -> ATCCAGT - InDel mutations (Insertion or deletion mutations) - Either jamming in a nucloitde where it wasnt there before - Or forgetting to add one where it belongs - Different from point mutations because these change the length of the nucleotide sequence - ATGCAGT -> ATGGCAGT - Repeat number Mutations; - Some parts of the genome are more susceptible to mutations and where it is is when there are repeats on the nucleotide sequence - The DNA proofreading can loose track of where it is and leave out or add a repeated sequence - ATGATGATGATG -> ATGATGATGATGATG - Chromosomal rearrangement (Inversion) Mutations; - Sometimes there are break in the DNA and when the repair mechanism goes to fix it, it in areas with very similar genetic codes Proof doesn't know which way is front and back and can reinsert the code backwards  - ATGCAGT -> TGACGTA - Identifying Mutations; - Pretty hard to do it butttttttt - Trio study; - Kinda brute force (like me studying bio) - You get two parents (sexually reproducing ) and one of their kids and sequence all three of their genomes (or the part you want to focus on) - Then look at the kid and look for a genetic change where there isn't one in the parents (eg the kid has a C in an allel where both parents are TT) - This is a mutation! - Identifying rates of new mutations; - We’re talking over a single generation here; - Mutations happen at a rate of 16 in every 1 billion nucleotides - Humans have 6 billion nucleotides (3bill per genome copy + diploid) so about 96 mutations per person (zygote) - Now in 8.2 billion people each base pair will be mutated 131 time over in each generation - Thats a whole lot of new cornucopia of mutations that wasnt present in the previous generation - Evolution doesnt have access to all this mutaional diversity because humans are geographically seperated - Mutation effect review (Thanks Silvia) + how mutations on genes work and are phenotypically expressed ; - You have DNA; - There are coding and non-coding regions - If a mutation in a triplet (codons) on a non-coding region it wont matter as it wont be expressed - If you have a mutation on a gene and it causes a different amino acid to be produced then it will likely have a downstream effect  - If you have a mutation on a gene but it doesnt cause a different amino acid then it wont cause any phenotypic changes but it is a mutation nevertheless (silent substitution) - (rates of) Mutations affecting fitness in eukaryotes; - Non-silent mutations will likely have some effect on fitness - Humans have higher mutation rates than flies but a bigger genome doesnt always mean higher mutation rates - There rate of mutation is higher than the rate of mutations that affect fitness (more mutations happen, but less of them actually affect fitness) - Theres a gene in flies that cause them to grow legs out of their heads instead of antenna and less obvious mutauins can have big effects on fitness and evolution o - G6PD Deficiency; - Is most common enzyme deficiency in humans and an example of fitness affection mutation because it causes anaemia but protext from malaria (slight fitness advantage but at what cost) - Disease allele (A-) is caused by 2 amino acid change mutations - All the coding enzymes have a change in them but only 2 of them lead to an amino acid changes causing the mutation - - Fitness distribution rates; - All the values in the graph are below the ancestral relative fitness of 1 (meaning they are all deletreieous/bad mutations which more common than beneficial ones)  - There are some kind of bad mutations anad then really bad mutations that will cause big problems to the function of the organism - Think about playing around the guts of your phone, you’ll mess things up preeeeee bad more lieky than you are to do smtgh good to it - Independent assortment; - Generates lots of genetic diversity (whoohoooo) - Parent have 2 sets of each chromosome (diploid) then through meiosis they randomly split into haploid gamets with 1 copy of each chromosome - Mixing with other parent makes more diversity in the diploid that was not in ancestral generation - To calculate the amount of combinations (of gamate) take the amount of copies of each chromosome (diploid = 2) then raise it to the power of how many chromosomes you have (humans =23) - - Recombination; - During meiosis (prophase I) sister chromatids line up and swap sections of their DNA increasing genetic diversity in the same chromosome - There was a recombination event at every colour shift here - Heriditary before mendel; - Preformationsim; - Sperm or eggs had a formed human inside and came from one parent - Blendingin inheritance;  - You irreversibly mix up the maternal and paternal phenotypes and you make a new one that can never express the mat or pat phenotypes again (cant unmix paint) - The flaws; - No way for a beneficial muatuon to increase in frequency via NS - If you have a rly fit phenotype and mix it with a less fit one and have the blended kid there no way for that rly good phenotype to arise again - Mendel and his Good Green Peas (Discrete Variaion); - Blending inheritance would expect light green peas forevermore - But Gregor dearest crossed purebred green and yellow peas - Got all yellow pease in F1 generation, let them self-feltilise and F2 had 3 yellow 1 green pea showing green was homozygous recessive (need to have two of the recessive alleles to be expressed) - Concluded that discrete particles (genes made of DNA) one copy from each parent make up an offspring genetically diverse from parents - These are discrete (mendlien) traits (either or, has to be one or the other, discrete values) - Is made up of a few genes with major effects - You can measure dominance and recessive ness and the changes in allele frequency - Continuous variation (Complex/quantitative Genetics); - Complex traits are a spectrum of values that can vary, not either or - Height is an example - Genes with partial/incomplete dominance (cross red rose with white and F1 rose is pink) and lots of alleles affecting them can give rise to continuous traits  - Many genes with small effects, the envrionment plays a role - Can measure effect of NS on these traits Keywords for this section; - Wild-type enzyem: The “normal” type of enzyme found naturally in populations - Mutatn enzyme: has changes in amino acid changes from mutatuions compares to wild type - Continuous trait: made from lots of alleles contributing to the same gene giving rise to a lots of possible values - Discrete traits: made from not a lot of alleles contributing to the same gene giving rise to only discrete values - Particulate inheritance: Meshes with continuous traits, genes are inherited from parents and can keep their ability to be expressed but not always expressed in the offspring generation Lecture/Slide Deck 5; Models & Measurement - Population genetics; - Founded by R.A Fisher, J.B.S Haldane and S. Wright - The study of how genetic variation can help us understand evolution - Provided foundation for “Neo-Darwinisim” and “new Synthesis” - Mixed Darwins THEO and Mendelian genetics - Positeded key questions that guided the field to understand many ecological and evolutionary genetics stuff in the coming years - Forces that can influence patterns of genetic diversity and evolution; - Mutations; - Big Boss (Ultimate) source of genetic variation - DNA replication errors :p - Increase genetic variation in populations - NOT DIRECTED Y’ALL CANT WISH FOR BETTER GENES - Grey bars are people, black liens are its alleles  - Theres a mutation occurring in the grey arrow that gives rise to two ways of being, the black dot allele and its abscence - Recombination - Creates new combinations of past mutations in a single individual - 50% mom 50% dad mixes and creates lots of new combos which why even siblings are different! - Increases genetic diversity - Crossing over event causes mutations on a chromosome to be present on the same chromosome in the next generation (the thre black dots were on 2 diff chromosomes then theyre on the same one) - Mom and dad chromosome swap portions of their genes during crossing over - Genetic drift; - Change in frequency of an allele (gene variant) in a population due to random chance - Increases or decreases frequency by random chance, not selection - Decreases genetic diversity because you’re just changin the frequency of an existing allele, not adding a new ones/combinations - Random sampling basically means its been randomly selected to increase or decrease - More significant in smaller populations; - It can half or double the allele frequency or make it disappear entirely - Smaller populations have less genetic diversity to begin with - Random events have a bigger impact (eg, if individuals with rare allele dont reproduce, taht allele can quickly disappear)  - In bigger populations with lots of genetice diversity and different alleles this doesnt matter as much - Red alleles passed on, black ones are not - Natural Selection; - There are three types of natural selection; - Negative (purifying) selection; - Fitness reducing mutations are removed - When a new (fitness reducing) variant pops up through migration for example it will be selected againt - Decreases diversity because it removes harmful variant leaving fewer variants and maintains the benefical/neutral traits keeping variation stable and less varied - Positive (directional) selection (Adaptation); - A new fitness increaseig variant enters population and will be favoured by selection and increase in frequency - Eventually because its so good it will become fixed and the polymorphic locus will become monomorphic with the population homozygous for it and it will become fixed - Reduces diversity because it increase the frequency of just the singel same allele - Balancing selection (Selection favouring diversity); - Selection directed towards increasing diversity - Heterosygot advantage (eg sickle cell anemia, you have one SCA allele and one wild type allele and  so you dont get SCA (wild ype is dominant) but are also more protected against malaria than people with two SCA/two WT alleles) - Increases genetic diversity becuase it is favouring heterozygotes with survival advantage - Migration (gene flow) - Movement of genetic material from one population to another - Like pollen blowing out to anothe rplace or people moving to new places - Increases diversity within populations, decreases it among the populations - - - How do we measure genetic variation - Heterozygoxcity (H) - An individual has two or more different alleles at a particular gene locus - Sample a population and see how many are heterozygous for that particular point (locus) of the genome - Eg population of 100, 25 are heterozygous at locus X so heterozygocity is.25 or 25% at that locus - Repeat for all loci of genome you are interested in - Polymorphisim - The presence of multiple alleles (version of a gene) within a population leading to variation in that trait amongst population - Polymorphism is about the variety of alleles in a population - Heterozygosity is about the combination of alleles in an individual - A gene locus can be polymorphic without being heterozygotic - What maintains genetic variation; - Mutation selection balance  - Genetic variation is recent and bad and selection will remove it - Only reaston variation exists is because mutations keep adding them back in - Selectin maintainin variation; - Basically balancing selection - Genetic variation exists because its good and benign selected for - Heterozygote advantage - Fitness varies so much over tiem and spac ethe only way to survive is to have lots of variation - Frequency dependent variation wher ethe rare allele is the most fit and will become the most common but then the other ones become rare and so they become more popular and on and on, so itll favour intermediate combos of alleles - The two schools of thought (if only it were that easy to think) - Classical school; - Morgan and Muller - Low heterozygocity (there would be low genetic variation so fwere differences in individual genetic makeup) - Low polymorphism (same idea, there would just be one optimal genotype and any variant would be less fit and selected against) - Wild type is normal genotype (because its the most common so it must have been the optimal one) - Selection is typical negative (purifying) - Balance school (such a sweet name imo) - Dobxhansky and Ford - Heterozygote Advantage - High heterozygocity - Hihg polymorphsims - Selection favours diversity - All of these increase diversity so this sis what balance school thought - To try and see who was right and meausr egenetic diversity they would go out and look for simple systems wher eorgamsisms displayed simple  medlin genetics so you could look at their phenotype and know their genotypes (Eg snail shells) - Morpholocical - They also looked chromosome inversions of squashed chromosomes (cytological) - Model systems in ecological genetics; - Butterflies and moth wing patterns adn flower colours are discretelat mednidelan genetics that were pretty big models - How much genetic variation exists in natural populatiosn and why; - Instead of focusing on mendealin genetics focus on continous traits - Impost artificial selection on different groups of organisms - Involves controlled breeding of individuals with particular traits for many generationes - So basically you impose some hardcore artifical selection on an orgamsim and look at the evolutionary response if thers not much variatoin you’ll stop seeing a response to selection very quickly, if there is lots of variation then you’ll see response to selection going on for a while - People did this experiment in fruit flies; - The selected for fruit flies with high bristle numbers fro 90 generations and the number of bristles just kept increasing (lots of variation in population) - However when they stoped imposing selection the number of bristles lowered and that seems to indicate that the alleles that made more bristle possible were probably deleterious otherise you;d keep the high bristles, maintaining the high bristles must hav ecome at a cost - They did the smae thign where they took corn with high and low oil content and bred them separately for thos characteristics and then when they relaxed eselction they quickly went back to the mean ancestral value - All this seems to point to deleterious variation  - We still dont know who’s right, we dont know if thers a lot of variation out ther in intermediate frequency (balance school) or if we just impose selection to increase the frweuncy of rare alleles (classical school) - Selection responded indicate taht there is lots of genetic variation for polygenic quantitative traits - No direct measurements on polymorphism or heterozygocity - comparative studies difficult as traits studied often are group specific - Richard Lweontin and the Electrophoresis Revolution (a nancy drew or sherlock holmes novel i’d read); - Richard and a collaborator named hubbay discovered a way to directly measure allelic diversity - Allozymes are different alleic forms that make the same protein - This was gel electrophoresis; - It could be used to identify what 2 copies of allele an individual has - You take issue from an organism, grind it up and mix it with a biochemical acid the drop it into a well in agaros gell - Then you apply a charge with polarity and the speed with which the molecules move across the gell give us information about the allese they possess - So individuals with just one blob on a line are homozygous for the fast or slow trait - But ones with one in each are heterozygous for the fast and slow allele - You can get information about polymorphism and heterozygocity in this way because you can see the frequency of it in electrophoresis (how common it is for an individual to have the same allel, differen alleles, how many slow vs fast in population etc.) - Advantages; - MAnay loci can be examined - Can be used in almost any organism - Loci are codominant (we cant detect dominance, only the presences of heterozygocity) - It examines protein level which is very close to DNA level - You can use it for comparative studies across groups (provides genetic marker loci for other studies) - People did it for a lot of stuff and found high genetic variation but this did not prove the balance school theory - Motoo kimura posited that having genetic diversity isnt good ro bad but just neutral, if it was bad selection would remove it all, if it was good selection would just fix it so maybe its just neutral because what ever is left varying is just there (v contrevisiol at the time) - Now we have DNA sequencers that can look at DNA at the nucleotide level to help use distingush between the three ideas - Can see what base is where in the dna - Can distingius, nonsense, misense and silent mutations - Some organisms have lots of variation and you can see thers just a lot of dna variation out ther ein general - Teosinte and corn (a-freaking-gain, why is there so much corn in this course) - Genome of corn and teosinte weremsequenced - They were looking for DNA polymorphsim (variety of different alleles for the same locus) - Corn has reduced genetic diverstyi compared to teosinte (polymorphism present in teosinte is reduced in corn) due to genetic drift  - A bottleneck event happened when we domesticated corn and those few individuals became corn - Arabidopsis plants colonised places with no glaciers and when the glaciers receded they colonised those arees and lost a lot of diversity due to genetic drift - Humans are the same, as we moved out of east and central africa to colonise the americas we lost genetic diversity due to genetic drift and a botlenecking event Keywords for this section; - Heterozygocitiy: an organism that has two different alleles for the same gene at a locus - Polymorphisim: presences of multiple different alleles for a particular gene within a population - Locus: location on a chromosome - Bottlenecking event: when a populations size drastically decreases lowering diversity as less individuals survive and reproduce and the genes fo the surviving individuals become more common effecting the populations ability to adapt to new environments Lecture/Slide Deck 6; Sex, Reproductive Systems, and Evolution - Introduction (Reproductive modes) ; - Reproductive systems; - Asexual; - Reproduces from a single mother and offspring are a complete genetic CLONE of the mother (meiosis) - Can get diversity from mutations - Parthogensisi; - Embryo develops from egg without fertilisation - Colonal propagation;  - Vegetative propagation, reproduction that doesnt involve seeds - Liek when you cut a part of a plant and put in water and it grows a new plant - Sexual; - Sexual reproduction involves the joining of maternal and paternal DNA to form a zygote (yes meiosis) - Dioecious sexual reproduction; - Like us you have 2 different sexes - One has bigger gamete one has smaller - Lots of plants and most animals are dioecious - Hermaphrodites; - A single organism has male and female reproductive parts (able to make both egg and sperm, or pollena nd ovule) - Very common in plants - Self-fertilising hermaphodites/selfing; - Can reproduce with self by combining the male and female gametes it produced to form a zygote (different from asex because we still have the combination ofpollen and ovule to make zygote, offspring are not clones) - Cross Fertilising hermaphodites/outcrossing; - Plants can also send out their pollen to fertilise ovule of other hermaphoditic plant - Daphnia; - Water fleas that are facultatively sexual meaning they can make partogenic egges or undergo meiosis to make gametes then mate andn sexually reproduce - Asex or Sex depends on envrionment but mostly asex, unles send of season in temperat climate - Water Hyacinth - Invasise weed  - Reproduces colonially and sexually (can recive and send out pollen) - Facultatively sexual - Why have sex; - If you can reproduce asexually why have sex. Theres a great cost to sexual reproduction - There must be costs and benefits to sexual reproduction - Costs and Benefits of sex; - Two-fold cost of meiosis; - We usually focus on female when talking about the evolution of sex - Sexual reproduction; - Female cretes haploid eggs that only become diploid when fuse with sperm but still theres only 50% of her genes - She only contributes half (4 in the image) of her genes to the next generation - Asexual reproduction; - Female parthogenically creates 4 eggs (diploid from the start), all are diploid and genetic clones of her - This is a great genetic and fitness advantage because hse is able to transmit 100% of her genes into the next generation (8 copies in the image) - Transmission bias; - Favours asexual femals over sexual females because asex femals contribute more of her genes to the next generation - (Ill take the) Unfavourable combination of Alleles (combo please) - Asecual reproduction can maintain favourable combination of alleles - If you have two homosygotes that are well adapted to different climates (for example) and you have them sexuall reproduce, about half o the next generation will be  heterozygotes (which are not well adapted to either environment) - So heterozygocity can break up favourable alle combinations while asexual reproduction can maintain them - Costs of finding mates; - Cant find a mate sitting on the couch eating chips people! - Energetic costs in the act of mating - Risk of predation while finding mates or mating; - Imagine a bright spier showin all its bright colours then getting eatin by a hawk :( - Infections; - Where there is sexual reproduction there will be quickly evolving STD’s looking to transmit their own genes 🙄 - Costs of producing males; - At the origin of life there were no such things as males cuz asex is perfectly viable - So why sex! - Benefits; - Favourable Allele combos more rapidly through sex - Just as sex can break up favourable allel combos, it can give rise to favourable allele combos much faster than asex - If you have a fit genotype which is ABC, with asex you have to wait fo mutation A to arise then fro mutation B to arise in the same individual with mutation A THEN you have wait even LONGER for mutation C to arise with someone who already has AB mutation - its a cruel waiting game - But with sexual reproduction when muatition A comes up quickly B and C will show up and then they will mate and quickly you’ll  get AB and AC which will mate and then you get ABC really quickly - Combining favourable alleles and getting rid of harmful mutations - Helps get rid of bad variants - Say you have two good and two bad alleles; - Asex will have that cloned over and over till a mutation gets rid of them - But sex will combine them to have offspring with all really good ones which will have a fitness advantages and offspring with really bad ones that will have bad fitness and be purged from population - Lottery models - Tangled bank hypothesis; - Spatially heterogenous environments - You have offspring and you dont really know where they will land so having them be heterozygous and adapted to two different climates will be helpful for them to survive - having a variety of offspring increases the chances that some will survive and thrive - some offspring are more likely to find a niche where they can survive and reproduce, even in a crowded and competitive environment - Red queen hypothesis; - Things arent uniform over time (temporarly heterogenous environments) - Say extrem wetness then drought, having variation in the population means that at least some orgamsims will survive - Always have to be changing to stay in the same place  - organisms must constantly adapt and evolve not just for reproductive advantage but to survive against ever-evolving parasites and diseases - Causes and consequences of sex; - Very hard to study why have sex - Oenothera; - Evenin primsorse able to asexually create seeds (~30%) - Lots of asexual species are pretty recent - Asex EP have higher rates of premature stop codon which are (deleterious) muatuons that can cause issues in amino acid sequences coding for proteins - Higer protein evolution rates (because of more premature stop codon mutations) - IMplies greter acculamtin of deleterious mutations than sexual organims - What causes the evolution of sex; - Rotifer (clsoe relative of daphnia) - Facultativel sexual (can be sex or asex) and the propensity for having sex is heritiable - Some UoftT people! Did an experiment - They took rotifers and put them inthem in environment A and switch between two diff tanks of environment A - THey did the same thing with environment B - Then in the third treatment group the switched between A and B to mimic spatial heterogeneity - If lottery hypothesis is right we should see increase in sexual reproduction which we did, when switchin between same environment they preferred  asex, when switching between different environments they preferred sex - AA and BB saw drop in propensity for sex but AB saw that propensity increase - Macroevolutionary History of Asexuality; - Asex by parthogenisis; - Not very common in animal kingdom - More common in invertebrates, rare in vertabrates - Asex by colonel propagation; - Very common in plants - Few if any species are solely asexual, they almost always have a way to sexually reproduce liek with flowers - Asex species are usually at the tips of phyloginies; - Suggests long term cost of being asexual - You might accumulate too many deleterious gneetic mutations and go extinct and have low genetic variation - Macroevolutionary pattern indicates higher extinction rates - Bdelloid Rotifers; millions of years without sex? - Very old and no one has ever documentated a male - Genome sequencing shows very clear signs of recombination that con only happen through sexual reproductin so theres gotta be a male out there somewhere….. - Causes and consequences of inbreeding and outbreeding (sexual organsims); - Oubreeding; - Breeding with others less closely related than random - Inbreeding; - Breeding with other more closely related than random - In nature theres a continuum between inbreeding and outbreeding - Talking about hemaphdites mostly here; - Outcorssing; - Mating with someone else either in or outbreeding - Fusion of gametes from 2 parents  - Selfing; - Mating with yourself (only possible in hermaphrodites) - Rly extrem inbreeding - Fusion of gametes from 1 parent (mixing up the genes but in a bad way) - Plenty of potential for inbreeding; - Orgamsins cant disperse too far so over time members of the same family will mate with eachother - Hemaphodites can mate with themselves or outcrosss - Really small populations may have no choice and have to mate with relatives - Inbreeding is bad!!! - Inbreeding avoidance traits; - In plants; - Time offset meaning the plant will produce pollen and ovules at different times - Your own ovule and pollen being incompatible with eachother - In animals; - Dispersal meaning that one sex tends to disperse very far in order to avoid inbreeding - Delayed maturation meaning by the time the offspring are sexually mature the parents are no longer reproducing - Extra pair copulation is basically cheating via diversifing mates - Kin recognisinaing and avoidances - Population genetic effects of inbreeding; - Inbreeding increases homozygocity and decreases heterozygocity - But it doesnt change polymorphism - So basically using that equation you get the genotype frequencies, but when you have inbreeding which increase homozygocity and decreases heterozygocity you have to add an inbreeding coefficient - You can see in the chart that with inbreeding homozygous genotypes are of higher frequency but in random mating the heterozygote is of higher frequency - But the polymophsims (frequency of the alleles) stays the same - Effects of inbreeding on rate of heterozygocity depends on mating patterns; - Inbreeding decrease heterozygocity, increases homozygocity and the effects will be cumulative with each generation - You keep losing heterozygoocity until you stop inbreeding - The more closely related the worse the inbreeding - With selfing you lose 50% heterozygocity each time - You keep losing heterozygocity until you stop inbreeding, you wont het the heterozyogcity back but you can stop it - Inbreeding depression; - Reduction of fintess of inbred offspring compared to outcrossed offspring - Lower viability (survival) - Lower fetilirty (reproductive output - Stron inbreeding depression disfavours inbred offspring, it favours outbred offspring - Causes soem bad phenotoptic traits - Inbreeding depressino ca cause loss of polymorphism but not inbreeding itself - Why can inbreeding reduce fitness; - We have rare but really deleterious alles which are recessive and often masked because theyre almost always in the heterozygous form - But with inbreeding will make them homozygous and expressed in the phenotype and visible to selection which will then wipe them out reducing the amount of alleles - Genetyic consequences of inbreeding;  - 50% reduction of heterozygocity per generation - competition between homozygous geneotypes and genetic drift for small populations can reduce polymorphisim - Inbreeding depression caused by homoszygozity for recessive deleetrious alleles - Why has selfing evolved so many times then? - Much liek the transmission bias in sexual vs asexual organims you have somethign very similar at paly with hermaphoditic plants - The oucrosser only gets two of its genes out into the world - The selfer get 3 of its genes out in the world, from the pollen and egg it fertilises in house and the pollen it sends outto fertilise other plants - Capsella sister species; - One is an obligate outcrosses the other an obligate selfer - At any given point on its chromosome the DNA diversity for the selfer is lower than for the outcrosses because voer long periods of time, inbreeding depression causes the loss of polymorphisim - Diversity takes a major hit over time - Selfing increases the accumulation of deleterious mutations - Understanding the frequency in nature of selfing and outcrossing; - Short term; - Selfing can be great over the short term because you can reproduce with yourself if no one else is around - The transmission bias that allows you to leave more of your gene copies in the next generation - Good if you already have low rates of inbreeding depression - Long term;  - Long term selfing can lead to inbreeding depression; - lowered genetic diversity - increase in extinction rates - Inefficent selection (because accumulated deleterious mutations will be sleected against) - This is why selfing species are quite fairly new and at the tips of phylogenetic trees Keywords for this section; - Inbreeding depression: reduced fitness of an organism due to inbreeding compared to outcrossed offsrping - Selfing: the ability to mate with yourself, sexual reproducation but male and female parts, eggs + sperm or pollen + ovule, very common in plants/hermaphodites - Outcrossing: Sexual mating with someone else, can be in or outbred - Asexuality: non-sexual mating in which mother gives rise to genetically identical clones - Sexualtiy: sexual mating involving fusion of 2 gametes and mat and pat DNA Lecture/Slide Deck 7; Natural Selection & Adaptation - Introduction (definitions); - Fitness; - Relative quantity which is the genetic contribution of individuals to the next generation relative to other individuals as a result of varying viability and fertility - Selective advantage; - A way to quantify fitness - The amoun by which some individuals of a given genotype are bette radapted to survive and reproduce relative to other in the populatin of a given envrionment - Adaptation - A trait that contributes to fitness by increasin the organims ability to survive and reproduce in a given environment (noun)  - Compared to ancestoral state - Adaptation is linked to environment, whats good in one place may not be good in another - An evolutionary process that leased to the origin and maintenince of a trait (verb) - Natural selection - Selection - A force applied to impose differential fitness on organisms - Artificial selection - Selection imposed by humans towards a goal - Domestication of plants adn animals - Attenuated vaccines (select for least virulent strain) - Selection experiments in genetics (fly bristle experiment) - Natural Selection; - Differentiation between alles but there is no goal in mind - Living and non living environment does the selection (eg climate vs survival from predators) - Affects all organisims including humans - Natural selection on alleles; - Positive (directional) selection; - Adaptation - Even small selective advantages (1% or less) can spread through populations with enough time - Wil lreach fixaton as frequency approaches one - Small differences in relative fitness can have big evolutionary effects - Negative (purifying) selection;  - Aims to remove deleterious alleles from teh population to maintain overall health and fitness by reducing harmful gneetic variations - Balancing selection; - Aims to maintain diversity - Heterozygote advantage - Frequency dependent selection; - Rare allel is better so more common ut other become rare and on and on - Many phenotypic traits are polygenic and show continuous distribution; - Slection acts on hundred or thousands of alleles at a timenot one by one - Get comfy with the graph - It shows the frequency distribution of a given trait in a population - X-axi is the trait, y-axis is how many in the population have that trait - Most continuous traits have this kind of distribution where the mean value is in the middle (higest value/most people have it) and off to the sides you have fewer individuals with those values - Modes of selection on quantititive (continous traits) - How does selction act on individuals on different parts of the distribution - Stabilising selection; - increases the distribution of individuals close to the mean and decreases variation in continuous traits - Disruptive selection selection; - The extreme phenotypes have the highest fitness  - Distribution increases in variance - Becomes widers in tails and has a divot in the middle - Fewer individuals with mean phenotypes, more with extreme phenotypes - Multimodal (two peaks) distirbution - Directional selection; - Only one extreme phenotype is the fittest - Theres a shift in the mean, not variance - Disruptive and stabliaing cause changes in the width of distribution, the variance - Directional causes changes in the mean, it just shifts over - Stablising selection on human birth rates; - You see a pretty symmetric distribution of birth weights - Overlaid in infant mortality rates where there is an increases in infant mortality at the two extremes - Stablising slection favours the average in teh population - Directional selection on beak size in galapagos finches; - There was drought when the study was condutcted - As the abundances of seeds dropped, finch population dropped and seeds became harder  - So this put strong directional selection to favour the birds with bigger beaks that could eat those harder seeds - Positive slection (increasing the frequency of a beneficial allele) - Disruptive selection in beak size in africain finches - Where they live there are either really small or really big seeds - So disruptive selection will favour the extremes, the birds with really big beaks and really small beacks toeat the really big and small sedes - You dont really see birds with an intermediate medium sized phenotypic beak - Disruptive selcetion toward two differnet extrems can be an early step in speciation - Studying adaption; - How to study adaptation; - Correlational studies; - These show how alleles are changing across space and time as a function fo the envrionment - But its not causation and there are limits to correlational studies sot they ar often complemented with other studies - Genetic studies; - These look for signatures in the genomes of a very strong selcton - Experimental manipulation; - Manipulation the environment/ecology which can be a big pain - Struggle to determine agents of selcetion;  - Theres lots of evidence for fitness differences and evolutionary changes but there not a lot of evidence for what the actual cause of these changes are - Very hard to link evolution to ecology - Eg large rabbits are better than big rabbits but why (would be hard to manipulate envrionment for higher and lower fox predation to get causality - Studying adaptation: environment-organisim correlations; - The peppered moth and industrial melansim; - Naturally occurring polyomorphsim for light and dark moths - The dark form was a dominant rare allele before the industrial evolution - 1850’s and industrial revolution start producing a lot of soot that would blacken the bark on trees causing a physical change to the moths environment - So directional selection increased the frequency of the melanistic moths because of their selective advantage, they are less likely to get eaten in the city because they blend in with the dark sooty trees - In rural areas with lighter bark and less pollution the moths were also lighter so they could blend in - After introduction of clean air act;  - As the soot concentrations went down the melanistic moth population also decreased as expected - There was a lag caused because its hard to get soot off trees and its a dominaitn trait which makes it hard for recessive alleles to become the main form - Evolution of heavy metal tolerance in plants; - Mine waste is usualt dumped nearby called tailings which are very bad for the environment - Nearby plants with tolerant genotypes (low frequency n=in nearby pastures) colonised tailing dumps and were abole to flourish in this competition free environment - The plants evolved to reproduce at different parts of the season from pasture plants so that those other alles dont come in and swamp otu the resistant adaptations - The graph shows the concentration of zinc near and way from teh mine and the frequency of the tolerant alleles which are higher near the mine and tailing but lower by the pastures - G6PD Defincy in humans; - We can see natural selectin by looking fro genetic signatures in teh genes of organisims - The enzyme deficiency causes anaemia but also protects against malaria - VVV good if yours heterozygous high fitnes because you have protection from malaria but youre not anaemic - Predictions of natural selection on this allele are that if you are in a place with no malaria it will be selected agains  nad in low frequency which is what you can see from geography - Selective sweep is when a new and beneficial mutation increases in frequency so rapidly because of its increased ability to survive and reproduce and nearby genes (whcih may not be beneficial themselves) are carried along because they are close to the beneficial mutation (they also become more common because of this) - It shows strong recent natural selection because it shows the particular trait has increased in frequency rapidly and the hitchhikers would not be present if now recent because recmobination would have broken them up over time - Shows directional selection because its a beneficial mutation which positive directional selection wants to keep and increase - Evolution in the lab; Experimental evolution; - 1n 1988 took a single starin of ecoli and split it into 12 different flasks of growth medium and never let them com into contact with eachother (no migration or gene flow) - Everyday a grad student would take 1% of the ecoli and put it in a new growht medium - Every 500 generations theyd freeze some ecoli for a fossil record and then take them out to meausre their relative fitness with their descendants - We can see that the descendants have adapted to their growth medium and have higher fitness than their ancestors - All populations rapidly increase in fitness and there were similar adaptations across populations (larger cell sizes, higher max rates on glucose) - Paraller mutations in the smae genes - Some unique adaptation and distinct genetic changes Keywords for this section; - Stabalising selection: increases frequency of traits close to teh mean and decreases variation in coninouts traits - Disruptive selection: Favours extreme traits which have the highest fitness and increased the width of trait distribution - Directional selection: Only one fittest genotype, selection causes a shift in distribution to have the mean be that trait - Correlational Studies: show the changes in allele over space and time as a function of the envrionment, but not causation - Genetic studies: Looks for evidence of strong selection in genome - Experimental studies: Manipulation the envrionment/ecology to study changes Lecture/Slide Deck 8; Population Structure: Genes & Phenotypes - Introduction (definitions); - Rat sneks; - We’re thinking about evolution which occurs on the population level - Rat sneks are found throughout north america and they have different patterns based on where they live… but why! - Is it something to do with their environment that they have adapted to - Is it because theres soem geographic barrier preventing them from sharing genes and beomcing more similar? - Definitions; - Population; - A group of individuals of the smae species occupying the same area at the same time, allowing the to exchange their good ol’ alleles - Migration; - The movement of individuals from one population to another  - Gene flow; - The movement of alleles from one population to another - Key questions for understanding geographic differentiation; - What forces influence the genetic differentiation of populations - How is diversity distributed within vs. between populations - What forces influence the phenotypic differentiation of populations - Can we distinguish genetic from envrionmental effects on phenotypes - Genetic differentiation of populations; Gene flow; - IMPORTANT DIAGRAM (keep DIVERGENT SELECTION, for the cue cards); - Two geographically seperated populations that have adapted to their local environment - They become different due to natural selection which will cause them to diverge - Genetic drift is another factors (the change in frequency of certain traits/alleles due to random chance) - The populations will be pulled apart via divergent selection which the accumulation of differences within a speices sometiems leading to speciation - BUT - The populations will be held together by gene flow which is the movement of alleles from one population to another - Some individuals may migrate or pollen or whatver but gene flwo will reduce the genetic diversity between those population - Gene flow will work agasnt adaptation because its introducing new alleles which have been adapted to a differnte evnironment in an population that already ahs adaptations for its environment - How to measure gene flow; - If we want to know how gene flwo influenecs populatin differnetiation we need to measur eit but thats kind of a pain - Difficult to observe; - Gametes can disperse but not actually breed - We can use an experimental approach; - To answer how much gene flwo occurs between geographically seperated populations we can conducted a froggy froggy experiment - We set up two geographically separated populations, lets say of frogs - One is homozygous for fast allele, other is homozygous for the slow allele - Leave them alone for a few generations then look for heterozygotes because the only way to get those is for gene flow to have occured - TRANSGENIC GENES FOR CUE CARDS - Gene flow between crop and weed sunflowers; - Loren reseberg UBC prof did a sunflower experiment - Peopel were introducing transgenic crops (which have DNA from another ogramism introduced to its genome) and were worried about those genes going into wild populations - He found a sunflower crop field homozygous fro a certain allele and wild sunflowers are homozygous for the alternative allele - So he plants experimental plots of the WILD sunflowers different metres away from the crop fields and looke fro heterozygotes - He found lots of them close by but the further he moved away the more they declined (exponential decline)  - 1) documented gene flow out of agricultural population into wild ones and - 2) the further you move away the quicker the appearance of gene flow drops (quantititve evidence of risk of gene flow) - We can look for neutral genetic markers; - By looking at loci which are neutral to selection we can separate geneflow from selection because we otherwise wouldnt be able to tell if the variation is due to selection or gene flow which can often work against eachother - Genetic differentiation of populations; Genetic Drift; - Probability; - Genetic drift is the change in frequency of certain traits/alleles due to random chance - Like you cant predict the getting an even or odd number on a dice (equal chance of each) - you cant predict whether a trait will increase or decrease in frequency from one generation fto the next - What does random mean in evolution; - Random means unpredictable; - Mutation - Recombination - Genetic Drift - Deterministc (predictable and non-random forces of evolution; - Natural selection - This is because if you apply selection for a particular phenotype you can predict where the population will go are long as you’ve got VHD - Stochastic (random) processes resulting in a loss of diversity; - Genetic drift; - Random changes in allele frequency (with respecti to environment and genotype) due to random variation in fechundity (fertility) and mortality - Gentic drift is most important when populations are small because they already have less diversity to begin with and genetic drift reduces diversity (because it just CHANGES frequency of EXISTING alleles it DOESNT ADD anything new) - Population bottleneck; - A form of genetic drift that occurs when thers a sharp decline in the size of a population due to things like famine/natural disasters - The remaning population will have much lower diveristy than the original population - Usually followed by rebound but not always - Just literally think of marbles of different shapes/colours coming out of a bottles neck - Founder events; - Another form of genetic drift where a group of a population colonises a new area - Again reduced diversity (relative to og population) because only the individuals in this group pass down their alleles - NOT ALL DIVERSITY OF ORIGINAL POPULATION IS REPRESENTED IN FOUNDING EVENTS - Random fluctuations in allele frequencies in populations of different size; - The smaller the population the more relevant genetic drift is - Genetic drift can fix allele (to 100% frq, or 0% frq.) more rapidly in a smaller population tahn a larger one because each individuals genetic contribution is more significant - Thnink about the heterozygocity “Pp” if you have a few individuals with that heterozygocity then very quickly youll get homozygotes and lost that heterozygocity - Whereas in a bigger population the greater diversity in genotypes helps buffer against this loss - We dont expect genetic drift to go in one way or another but we expect it to go some way due to random chance - There are heterozygotes in the graph (the 0.5 on y axis) and you can see on the right in the smaller population you lose heterozygocity very fast compared to the larger population - Theres also less consistency of evolution - Explaini the graph; - So you see the og population with lots of diversity and then two founding events of the same size but different frequency of alleles - The first one grows more rapidly and that helps curb the effects of genetic drift - They will no