Bio Final PDF: Evolution and Genetics

-​ Evolution is the theory for origin of life: False: Evolution can only work when we have existing life, does not concern with about where life came from but about the changes of life about history of life on earth -​ Evolution gives rise to traits that species need for su...

-​ Evolution is the theory for origin of life: False: Evolution can only work when we have existing life, does not concern with about where life came from but about the changes of life about history of life on earth -​ Evolution gives rise to traits that species need for survival: False. Evolution doesn't give rise to traits, traits come about through mutations, sometimes traits are beneficial or detrimental, but selection can only act on variations that exist on populations already. Already have traits,existing traits, for selection to act upon -​ Disease genes are retained through evolutionary processes: True. Selection works on what variation exists.GEne flow,in one population that can be advantageous for one population can be neutral for another.A gene is only disadvantageous, if the selection happens before reproduction. ex) if you have alleles from Huntington's disease, might not manifest until 40, and might already produce. Those disease alleles can be maintained in population -​ Humans are still evolving by natural selection: True, average height is higher, continuous adaptations to environment conditions, trait preferences. -​ Evolution represents a gradual improvement of a species: False: Evolution doesn't care if traits being selected are making a better species, it makes them more adapted to the environment. But traits come from the cost of other traits Did Not gain extra traits, gained adaptations, lost ability to adapt to previous -​ Evolution is a slow gradual process: Usually very slow, but can be punctuated by rapid bursts or short reproducted life spans. -​ Extant: existing today -​ Biological diversity shows an interaction between the forms we know of now, but also forms that came from before. -​ Species are temporary:Extinction is much as part of the process of nature and the formation of new species. -​ To explain diversity : we use evolution Define Evolution: -​ Change in allele frequencies in a population over time. We can see it on a micro evolutionary scale.Alleles drive phenotypes and phenotypes get selected for in those individuals and populations. Studying evolution: -​ How inheritance work, traits passed on -​ Populations and quantitative genetics: How allele frequencies in populations and diff locations.changing environmental conditions, Looking for adaptations. Paleobiology: -​ Large scale evolutionary changes affect groups of organisms , very long periods of times, fossil record, how modern species developed from extinct species. Integration of genetics and morphology: developmental patterns and evolutionary transitions Charles Darwin -​ Made a voyage around the world interested in the natural world. >church> join the crew of the Voyage of the beagle > Keep the captain entertained.> Traveled around the world taking notes and collecting samples of organisms back to England > Eventually landed on the galapagos islands (powerful environment for studying environment, Volcanic activity and every island had life on it and had diff life on every island> came back to england Ideas that inspired Darwin: 1.​ Some species survive while others go extinct ( Idea written by Curvier, spent a lot of time looking at fossils) Curvier -​ Looked at species fossils and skeletons and comparing them with existing species, similarities and differences -​ Found species were going extinct and declining (BEcause of catastrophes, like flood), some species were surviving. -​ Evidence: extinct mastodon, related to modern elephants.Existence of fossilized bones from species that no longer existed. species that currently exist. 2.​ The earth must be older than believed and undergoing change ( Lyell) -​ “Principles of geology”,Earth had to be much older than the accepted age because landforms were not fixed structures because of catastrophic events because of slow geological processes. -​ Evolution takes a lot of time: Landforms, mountains and canyons forms gradually from geological process not catastrophes ( Don't suddenly crop up overnight because of a flood) 3.​ Species themselves must be capable of changing (Lamarck) Lamarck: -​ That species change over time through transmutation( not the idea that life was put on earth and will never change) -​ Mechanism: Traits that individuals acquire could be inherited and passed to offspring. Disuse of traits means losing traits.He looked at inheritance Individually rather than population. -​ Mechanism for change was wrong, but recognized species were changing like landforms slowly -​ Made darwin think of importance of inheritance of traits -​ Epigenetics ( How DNA is interpreted, gene never gets turned on and can change through diet and exercise and environment and be passed on) 4.​ Theremust be a pressure to force adaptation, competition for resources ( Malthus) -​ Humans pops grow faster than available resources so the “fittest” individuals survive -​ Always more people than resources to sustain will lead to competition and the individuals that are best able to compete will get resources and pass traits on. -​ Population grows exponentially, Food resources increase linearly because more people will work the fields but eventually because of limited space and reach a point where population is larger than what can be sustained by resources. Charles Darwin -​ Took the notebooks and preserved organisms, and started to write about them. -​ He wanted to make his theory sound and unassailable. Want to be right -​ What darwin Knew: 1.​ Idea of selection is being able to change species: take any plant or animal and select traits you want and breed individuals. -​ Artificial selection was well understood by this point -​ If we manipulate a species to change drastically (Dogs choose traits to be less aggressive and more protective) why can't this happen in nature blindly Observation That convinced Darwin that life evolved  -​ Finches from galapagos islands, samples collected from a small region by separated by water (what they ate, and their environmental conditions) -​ Big powerful beaks lived on the ground( Nuts and seeds to open) -​ Smaller beaks( insects and needed smaller beaks to eat) -​ Differences because of environment and different from mainland finches > must have adapted from mainland finches >Common ancestor for all life on earth Alfred Russel wallace -​ Came up with a theory of natural selection independently of darwin. -​ Both ideas published by evolution by natural selection On the origin of species by means of natural selection: -​ Population has variation in traits > Natural selection works on variation, by saying some of those variants of traits will be better suited for survival and lead to reproductive success > If those variations that exists and being selected for are heritable variations than those get passed on to the next generation of population and over time those variations become fixed> more fixed variations the more distinct that population becomes as a species compared to other related members of that population. -​ The struggle for existence from limited resources = favourable variations that improve your chance of getting resources will be preserved and unfavourable traits that limit access will be removed and destroyed in the population Life is tightly associated with the environment : -​ Process of natural selection is a blind process, evolution is not trying to give camouflage activities, trait is bein. Adaptations driven by environment they live in Case study of darwin’s finches -​ Noticed that species on islands quite closer together were quite different from island to island -​ Closer the islands were geographically the more similar the species were to another The galapagos islands -​ Islands are far enough away not many things can get there on their own, have to have assistance, natural drafts or driftwood. -​ Terrestrial species on these islands don't have many relatives nearby ( Cant move that easily) -​ Neighbouring islands will have close relatives -​ Between the Galapagos and the mainland there is very little gene flow: you can have particular genes and in a population, and this makes it a unique population because there's no exchange with a similar species. -​ Gene flow is limited in the galapagos islands because there's not alot of movement in between the islands and the mainland, no species into the islands and away from the islands. -​ Adaptation radiation: rapid evolution and adaptation from an ancestral species into a number of new species that are moving into a new environment with no natural predators or competition and expand out and fill diff ecological niches defined by the environmental conditions. Organisms diversify rapidly from ancestral species into many new forms -​ For finches, a small population of ancestral species coming from the mainland, bringing diff phenotypic variations within the founding population some of those phenotypes will be adapted to diff types of food and diff types of habitats. -​ Instead of coming to this new land and all competing for the same food, they spread out and adapt to whatever food is available A beak gene/ Heritability -​ To differentiate between species -​ This study gives the idea that if we have a gene that is linked towards a particular phenotype that we know is diff between diff species and has helped species adapt, because it's a gene and variation exists at that genetic level , so we know that variation can be inherited. -​ If a bird has a large deep beak the offspring will have large deep beaks -​ Natural selection does not require heritability, a trait can be selected for that is not linked for a gene and is not be inherited it won't lead to evolution by natural selection -​ NAtural selection is just choosing for particular traits that organisms have to give reproductive success. But if those traits can be inherited there won't be any change in species -​ Example, You get a haircut and you have a date, then you have a baby(Increased reproductive success). That baby won't inherit your haircut, if that particular haircut is something that your ladies like (attractive), that is being selected for, but you can't inherit it. KEY concepts -​ Evolution in response to natural selection is inevitable if: -​ There is variation in a trait -​ Variation is heritable -​ Some variants survive and reproduce more than others -​ Specific features of the environment can generate natural selection on a trait What darwin didn't know -​ Heritability (DNA) -​ How were traits inherited / offspring -​ Why is it you can have traits in a parent but not in child and skip generations Inheritance theories Blending inheritance: -​ Two parents produce an offspring, that will have a merged intermediate of parents -​ If there are 2 contrasting traits, as you mate individuals you get a blended form. Like black and white rabbit, it'll keep being lighter and light until white gain and black trait would become blended out -​ If blending inheritance was the mechanism : variation would be reduced overtime -​ But this didn't explain why this variation continued to be present in populations. Why did we still Have black bunnies in the population? -​ Black and white merge to make grey trait , gey trait would be passed on Lamarck: -​ “Inheritance of acquired traits”: Traits that were passed on were favourable or used by individuals very often/ unused traits would be less likely to be passed on. Gregor Mednel: -​ Tested hypothesis of blending vs Particulate inheritance -​ Used true-breeding varieties of peas ( always gave the same phenotype when self-crossed) -​ What was useful about using peas was there were several discrete traits that could be followed from one generation to the next: Phenotypes -​ Traits were predictability heritable from one generation to the next  -​ Goal: Could he predict the pattern of occurence through rounds (were they blending, disappearing or if they were remaining) -​ Mendel started with 1)​ True breeding strains (everytime u cross yellow seeded plants together you will always get yellow seeds) 2)​ Focused on a single trait at a time ( People were usually looking at all traits and looking like blends ) 3)​ Did a lot of crosses :quantity Crossing pea plants P1= All true breed, AA, aa (yellow and green) F1= Kids (yellow seeds were dominant and green were recessive ) Dominant Versus Recessive -​ Dominant allele codes for a functional protein where the recessive allele does not (pea colour is determined by an enzyme that break chlorophyll, that determines colour and if enzyme is present the colour will go from green to yellow) -​ Yellow (A)= dominant, green=recessive -​ Discrete trait > for phenotypes Segregation -​ F1 would always show all yellow seeds -​ Self fertilisation of those of the F1 plants ( makes F2) >Monohybrid cross we look at single gene and were doing a cross between two hybrids( heterozygotes) for a gene. -​ In order to conform idea of particular inheritance= green traits re emerging, and yellow traits also coming back -​ When he added all the numbers there was a ratio of 3:1 ( 3 times more dominant traits that recessive) -​ Mendel proposed: 1.​ Any of these traits there were 2 factors individuals inherited that governed phenotypes (allele) 2.​ Principle segregation tested by predicting the outcome of crosses (2 things coming together to make offspring phenotype ). Only one factor going on during meiosis. -​ Two alleles presence in parents (true breeding), AA and aa >kids Aa >segregation in F1 in order to combine to make F2 is where we see splitting -​ 3:1 Phenotypic ratio -​ Expected ratio of genotypes: 1:2:1 -​ 2 Factors were being split during the formation of gametes Question -​ Looking At all those F2 peas, the yellow of those ¾ are all of those the same? -​ He then self crossed those peas and he found that ⅓ of those pease ended up being true breeding ( only produced yellow seeds) Mendel's hypothesis -​ Adults must carry 2 copies of factors (genes), as discrete particles that can separate and come back together to govern the phenotype -​ Dominant traits will mask recessive  -​ Pair of alleles will separate during gametes being formed half gametes will carry one allele the other half will carry the other allele. Separate during meiosis and then recombination through fertilisation we will get all possible phenotypes -​ Diploid organisms get one allele from each parent Monohybrid cross : a cross between 2 heterozygotes for a single gene -​ F1 generation -​ Probability of a gamete inheriting one of the two alleles during meiosis is random gamete inheriting alleles (random alignment of chromosomes at metaphase plate) -​ Probability of those gametes coming together in a cross and genotype is also random that we can predict statiscally, by acquiring each gamete from mother and father. probability of A big A combining with a big A is gonna be ½ x1/2= ¼ Product rule -​ I that getting the probability from A parent is ½ and the other parents A (½ ) then the probability that those come together will come together is ¼ -​ When 2 outcomes are equal we need to add those together: Sum rule: -​ Formation of Aa and Aa in order to find the probability those individual probabilities needed to be added together. -​ Individual processes are added Mendel came up with a balanced way of doing test -​ Test cross: between an individual that is phenotypically dominant and a tester that is always homozygous recessive -​ If that dominant individual has any recessive alleles, we're gonna see those with equal likelihood in the gamete pool as the dominant allele.=1;1 ratio -​ Segregation of alleles observed by mendel happened during anaphase 1. Dominant is rarely universally observed -​ Incomplete dominance: intermediate phenotype, supports the theory of blending inheritance, but importance of mendel inheritance is that these traits are blending together but are existing as discrete particles that can be recombined in a late form. -​ One of the alleles are non functional the other allele is functional on its own in a heterozygote is not capable of not giving full phenotype -​ F1 phenotype is an intermediate from the p1 generation -​ Either of traits don't masks each other/ no dominance -​ At a molecular level, enzymes might be involved : not a clear threshold that if you have one allele you got a enough enzyme to do that. But if you have one it'll have on functional producing enzyme , itll make pigment but its not enough for the full phenotype, so it'll be a lesser phenotype that the parents. Codominance -​ Alleles have equal effects -​ Both are dominant alleles fighting for expression -​ Don't merge but have both -​ Ur getting the expression of both independently of each other We can have genes with more than 2 alleles (poly allelic) -​ Many alleles for a single gene ( there are a huge number of combinations, every version of these alleles will alter shape of proteins) -​ Immune protein that exists that exist on our cells, flag not to attack normal cells in body, many shapes of proteins based on alleles inherited, unique to you: -​ Rejection of a transplant more likely to share alleles with family than stranger -​ Variability in immune systems -​ Viral Outbreak that only targets one set of alleles if we have multiple alleles it increases a large number of survivability. MEndelian segregation preserves genetic variation -​ How you can have offspring that has dominant and skipping traits Discrete traits> “mendalian” -​ Often are the exception -​ Having a single phenotype that will happen every single time due to combination of alleles -​ 2 allele give u white eye, and if u have wild type you'll have red: doesn't happen very often Complex traits -​ Most traits exists as complex traits, phenotypes that exist on a spectrum looking at a distribution of traits than just yellow vs green etc. (height) -​ These are polygenic: A trait that has more than one gene controlling it. -​ If we look at single gene inheritance for something like body size, the more dominant big alleles you have the larger your body size will be. The single gene indicates 3 diff body sizes. -​ Ppl don't follow in two 3 heights tho -​ The more genes we add into this the more versions of phenotypes we have. -​ Other factors influence traits: 1.​ There's distribution within 2.​ Environmental factors that affect body size on top of genotype ( milk) -​ Mendelian inheritance is small subset -​ Genetic and environmental influences create continuous distribution Theme 4B -​ Although we can predict the single parent cross , in the population level we may not see this distribution of alleles -​ If you were to take all the sperm from all the population and eggs, you might find that 70 % A percent of 30% same for the female. IF you allow to mix you wont get a prediction of 3/4 dominant phenotype and ¼ recessive phenotype.MAth will be based on allele frequencies rather than individuals -​ The frequency of allele is not always the same ratio as the single cross Causes of evolution Mutations : introduction of new alleles, will change allele frequencies MIgration :intro frequency of alleles Genetic drift: randomness of survival, can have all the genes and alleles that would best suit survival but if asteroid lands on head that won't make a difference WHat would happen to genetic variation in the absence of evolution -​ No new alleles and changing phenotypic variation  -​ No natural selection acting on variants leading to reproductive success based on phenotype any trait being passed on are being passed on randomly -​ Not gonna be changing allele frequencies through mutations Hardy weinberg -​ If we look at mendelian inheritance and look at a single trait governed by a single gene (genetic locus) encoded by 2 alleles what would happen to those traits in the absence -​ If no evolutionary processes are acting on the trait, the trait should remain simple. Conditions that need to happen in order for an absence of evolution 1.​ No new additions to existing alleles to the population. If a single gene has 2 alleles we won't see a 3rd allele. = No mutation ( a single locus with 2 alleles does not change state between generations ) 2.​ Alleles aren't being added or taken away by the population ( through migration/emigration ) -​ No gene flow (migration, in or out) 3.​ The population is very big(infinite)- maintain allele frequencies -​ In the natural world random stuff happens in order to negate this random loss of individuals in a population. There has to be a large population in order to observe impact. And therefore change allele frequencies ( no genetic drift). unaffected in disruption if population is big -​ Genetic drift: change in allele frequencies that happen due to random process (effect small populations rather than bigger ones) 4.​ No natural selection taking place (Survival selection), for the trait -​ Regardless of genotype all individuals will have same fitness -​ Evolution of a trait rather than evolution of a pieces over time -​ Shouldn't be linked with survival and being selected for , allele frequencies would increase (in evolution), characteristics that don't have an impact on selection 5.​ Random mating: -​ Regardless of genotype all diploid of individuals have the same probability of mating HArdy-weinberg Equilibrium 2 alleles = A and a p= freq(A) q=freq (a) p+q=1 -​ If we have all conditions of hardy weinberg than allele frequencies would stay the same forever -​ Allele frequencies that exist in the gametes. Gametes come together randomly -​ The allele that either the sperm or the egg have is independent of each other it doesn't matter that if one sperm gets an the egg doesn't have to get A. Therefore in equilibrium : allele frequencies aren't changing 4c -​ All the way we do get changes in allele frequencies in a population: -​ Another major driving force of evolutionary process is drift: Chaos and randomness to change allele frequencies without paying attention to phenotype. But the individuals that remain out of that chaos will be there to populate the next generation and genes and traits will repopulate the future Genetic drift:  -​ Evolution by randomness( don't always see only those individuals well adapted to the environment going forward will create next generation) -​ Can affect the frequencies of genetic variants and traits during life cycles -​ Probability of occurrence should not be affected by and individual's phenotype -​ Impacts smaller population more (change in alle frequencies due to chance) -​ If we have a population that is randomly mating, in a small populations, we might get the same genotype and eliminate recessive alleles ( no more little alleles, alleles been fixed by random processes) -​ Reduces genetic variation Bottlenecks: forest fires that remove a lot of population (does not select based on phenotype) , individuals that are surviving all have an allele frequency that isn't the same as the starting population. -​ Allele frequencies used to make the bottleneck population are gonna be used to repopulate and if we lost specific genetic variants than those are gonna be gone and can't re populate Founder effect: -​ We have a starting population that remains but then we get dispersal of population as some members leave and settle to new areas, IE island dispersal events : galapagos islands with diff phenotype distributions -​ When the population grows the population will carry specific alleles and diff alles than we started with -​ In Humans we can look at all of our genes and asking how many of our gene loci are homozygous vs heterozygous.use as a measure of genetic diversity -​ Individuals with the highest mean heterozygosity, are individuals that live closes to starting point (africa), and further away you get the less heterozygous the gene loci are -​ Less genetic diversity the further away you get. Population divergence: -​ Where 1 population had a heterozygous genotype overtime through a random process, we get a distribution of more homozygous , the more genetic drift events we have the more likely alleles will get fixed. Founder effect leaves only to create a new population while bottlenecks are the original population. Non-random mating -​ Any mating between individuals that is governed if individuals are closely related or less closely related those drawn by chance Inbreeding: mating with closely related. Such as small isolated populations Consequences: -​ Does affect genotype frequencies rather than allele frequencies -​ Increase in homozygosity (recessive) -​ Rare alleles are more to come together within mating with family than higher the population -​ How many of those gene loci are homozygous, as we increase inbreeding coefficient the overall effect on the fitness of that population is going down. Less healthy lower fitness, less genetic variation Outbreeding: Individual deliberately seeking mates outside their family pool. Ex: pack of wolves. Assortative mating: Similar genotypes and phenotypes choosing to mate with each other more frequently rather than expected under random conditions. Natural selection : predictable change in frequency distribution of a trait between the parental and offspring generations as a result of 3: 1)​ Individuals vary 2)​ Survival and reproduction is not random : Galapagos finches(environments with food sources with big seeds, individuals more capable for breaking into the seeds will be more successful) 3)​ Variation is being passed on offspring (traits will continue to emerge) Pattern 1)​ Direction selection: One extreme phenotype is selected. where individual where they have extreme phenotype being favoured, over time it'll drive a change in overall distribution of phenotypes), Moths in natural habitat, that camouflage better survive better, rather than black moths that stand out to predators 2)​ Stabilizing selection: Selection favouring intermediate phenotype (ex, multiple ganges or incomplete/ codominance), favouring heterozygosity rather than extreme phenotypes selected against 3)​ Disruptive selection; Favouring for both extreme phenotypes : intermediate phenotypes are selected against No selection is taking place: -​ Fitness curve would be flat because there's no difference in fitness if you have different phenotype -​ No change in phenotype distribution -​ Changes would be because of random chance not selecting force Directional selection -​ If we apply a fitness curve that is favouring extreme large body size than small body, we expect to see a shift in the phenotype distribution -​ Losing variation at the small end and gaining more individuals at the higher end -​ We see an evolution of trait mean towards larger body size, positively affecting larger body sized individuals and negatively affecting smaller body size induvallas shifting the mean. -​ Deliberately selecting out phenotypes to favour extreme favour types and shift over time in a population (ex resisting pesticide) Stabilizing selection -​ Fitness curve is an acc curve that fours intermediate phenotypes, and selects against extreme phenotypes -​ We don't get an evolution of the trait mean, but reducting vairaiton in favour of the intermediate phenotypes, losing extremely small and extremely large individual -​ Trait mean isn't changing, but variance between generations is decreasing. -​ Average individuals have higher fitness Heterozygote advantage; -​ Tend to have a survival advantage over other homozygous genotype -​ Example: Sickle cell anemia and malaria >crystallisation of hemoglobin at low o2 concentration -​ A (normal), S(sickle) -​ Heterozygotes AS have a mild condition -​ Homozygote SS don't survive -​ For malaria, this disease tends to not to infect blood cells that have the sickle allele, individuals that carry the heterozygote and carry the sickle cell allele, have built in resistance to malaria -​ AA are normal but get affected by bad malaria  -​ In countries with higher malaria risk we see a higher frequency of the sickle allele in these populations. Disruptive selection -​ Curve where uts low in the intermediate phenotypes -​ We get 2 peaks in our curve, as a result for selecting for extreme small and extreme large size. -​ Trait mean of does not change but distribution of phenotype is changing between the extreme ends -​ Average individuals have lower fitness than extreme individuals Selection manifest? -​ Reproductive success is dependent on what biological sex one is. -​ Viability selection: have you survived enough to have babies -​ Fecundity selection: selection based on the ability to make babies (capacity for producing offspring) Sexual selection -​ Just about weather or not you can succeed better at making babies than other organisms -​ There is variability that exists within populations that doesn't seem to serve in any survival benefit therefore, must serve benefit in terms of sexual selection -​ BEcause there's a difference ein how gametes are produced there differences in how individuals producing these gametes are allocating their resources to go into production -​ Differences in parental investment :Eggs are expensive and sperm is cheap -​ Asymmetries when looking at parental care: -​ Cost of bearing (pregnancy) and raising offspring -​ Usually greater in females -​ Reproductive success: females are limited by resources(surviving long enough, food needed to raise offspring), males are limited by access to females Batman's principle=Males show greater variability in reproductive success, leads to significant differences in phenotypes between genders Sexual monomorphism: Phenotypes are less important mating Sexual dimorphism: there's a huge amount of variability between gender within species. A Lot of competition between species for males, we tend to see selection for traits that allow males to be more competitive. Females, try to blend in more and survive. Reproductive success= fecundity (ability to produce offspring)+ mating success (actually succeeding in producing offspring) you can high fecundity but not score a mating partner Sexual selection= goes broader than darwin's conception (where he considered arose because mating ability or fertilising ability as diff processes, sexual selection) -​ He struggled with this idea; he did recognize that things that produce the traits produced by selection sexually,are things that would often diminish survival. -​ Modern perspective of natural selection incorporates sexuals selection aprt of this becaus eht process doesn't change still have variability and more have reproductive success but get passed on.= but outcomes may change 1)Intrasexual selection: Fitness differences , sexual selection happening between members of the same sex where they compete for mating opportunities (larger males vs smaller males) 2)Intersexual selection: direct selection by members of oppostite sex. Preferential mating between males and females.( Selection for dances for females, how long males can do it ) Consequences of change: -​ When there is genetic divergence between isolated populations each of the populations will be subjected to things like ( genetic drift, founder effect and population bottleneck and mutation and differential selection) Independently of each other. -​ Need to accumulate fixed differences Reproductive isolation: Prezygotic barriers (stop mating, or stop fertilization to make a zygote) -​ Shape of an organism, habitat isolation, behavioural isolation (one mating display that has been selected for in one species may not be recognized by a similar species),gametic isolation, mechanical isolation -​ Mechanical isolation : where depending on what type of species that pollinate it can depend on Postzygotic barriers( mating does occur and production of zygote, but there are mechanisms from developments or reproducing ) 1.​ Reduced Hybrid viability: after fertilization takes place between 2 related species very often,the likelihood of that hybrid zygote surviving through development to be born or go through the adult stage is very low. 2.​ Reduced hybrid fertility: Hybrid is sterile.( need compatible homologous chromosomes to line up) 3.​ Hybrid breakdown: hybrids can mate and have good traits from parents and produce offspring but those offspring will have reduced fitness. So if we see either of these , we can think we are looking at 2 diff species Modes of species Allopatric speciation: -​ Staart with single population, will be split into 2 populations maybe through physical barrier.(vicariance).Can be separated by dispersal as well -​ Peripatric speciation:a dispersal event but its not splitting population in half rather we are seeing a small population break off and establish somewhere else. -​ Physical split is that we cease to have any gene flow and populations will go on evolutionary journeys independently.> accumulation of diff mutations, fixation of diff alleles -​ ENough of those alleles get fixed that those populations are no longer compatible together (cant breed). -​ Therefore speciation has occurred -​ If your remove barrier and they come in contact and they still remain distinct speciation has occurred Sympatric speciation -​ When there is no geographical separation of a population. Ancestral population stays in one place -​ Through disruptive selection where extreme phenotypes typically result in distinct subpopulations within the original population ,and eventually divergence happens to become distinct species. Off on their own journeys at the same place.individuals with the same phenotype would mate more with each other and two seperate species would form  -​ Initial stage:polymorphism (two forms adapted to eat diff foods, or diff preferences for mating, red and blue phenotype but no one wants to mate with the middle purple phenotype) -​ MAting between forms are discouraged Polyploidization -​ Ploidy can cause speciation because of errors during meiosis and you produce a gamete during rather than dividing in anaphase 1 in meiosis all chromosomes end up going into one cell. Create 4 cells 2 with no cells and 2 would have diploid gametes (supposed to be haploid) -​ If you have 2 organisms with a failure in meiosis and they come together and produce offspring they make a tetraploid offspring. Which is a new species. -​ 2n gamate+ 2n gamaate = autopolyploid ( can only mate with other autopolyploids= reproductive isolation) Morphospecies concept -​ Species that are defined by unique and reliable morphological characters by looking at species. Discrete types of organisms by unique characteristics -​ Advantage: practical and simple to use -​ Disadvantage:It doesn't exist on a genetic basis, just based on how things look. Choices of characters may be arbitrary and some species cannot be diagnosed morphologically since they look the same or there's just variation within a species that we cant tell -​ We can start looking at multiple different traits and comparing them, and cluster them to find species Biological species concept -​ Species are groups or potentially interbreeding natural populations that are reproductively isolated from other such groups -​ Advantages: clear criteria and evolutionary justification -​ Disadvantages: hard to track in field but less issue with genomics. But we see examples of species where they look like they don't reproduce with each other, but they do migrate and we have some gene flow by intermediate. Complexity -​ Our idea of a species is just a hypothesis.subjected to change, and one definition of species may apply to one organism may not apply to another organism THEME 5 -​ NEsted patterns -​ PHylogenetic trees: Shows relationship between species and provides a hypothesis for evolutionary relationships -​ Built based on data we have (dna, morphology, etc) -​ Nodes represent branching points -​ When drawing a tree if its an extitisting ng species we want to make sure the tips of our branches are aligned and if species went extinct that we prune back that branch to when the species went extinct -​ Sister groups are the most closely related species on a phylogeny. (common ancestors not shared by other species or groups) Phylogram: -​ HAs a time scale associated with it/ branch length will be varied based on when branching occurred Cladogram:  -​ Where time isn't factored in , branches tend to be equal in length (just branching) -​ We can build trees and show branching patterns for species but also zoom in to the individual level and infer info about diversity within a species using the info. To look at lineages of the individual -​ WHat set of characters will i use to build our trees? -​ we usually use character that we know that are shared between species : vary among species but not within species ( make sure were using beak colour, but were choosing colour that is not an existing variation and not variation where within species that there are variations) Character : morphological or DNA -​ When are looking at character that has a discrete number of character states -​ Ex: character: flower colour, character state: any diff flower colours, discrete and dont vary within that species -​ Use just presence or absence of character as character state : wings character state: diff shapes , style but you can also have if wings are present or not. -​ When choosing which characters to use when building the tree: -​ Consideration if the characters were looking at are homologous characters (shared ancestry and derived characters) -​ Analogous: Or character that look the same but dont have the common ancestry(often see of convergent evolution process, where there's a trait that is a good trait for environmental pressures and it merges through multiple pathways) -​ When choosing character to build our phylogeny choosing things that are homologies that evolve from a common ancestors are the better ones to choose -​ Using an analogous character = homoplasy this is where we run into issues (attempting to group birds and bats together, inaccurate). -​ When choosing homologies to define similarities between species we need to make sure we aren't choosing homologies that exist for all species in a phylogeny. Choose things that appear in certain parts in evolutionary history, but when we trace back we see examples of related organisms that dont have some of these traits= synapomorphies We need to consider the loss of traits based on the type of selective forces experienced Early atmosphere: -​ Reducing atmosphere, molecules that were present in the atmosphere would prevent oxidation through the removal of molecular oxygen storage in more reduced molecules like water , methane and ammonia. Without o2 chemical reactions needed an input of energy(enzymes, to create chemical bonds). Lighting would transform these organic compounds intp primordial soup -​ An oxidizing atmosphere has oxygen (O₂) and other gases that easily take electrons from other molecules. This kind of environment breaks down molecules — it's not friendly for forming complex, stable compounds like those needed for life.​ -​ A reducing atmosphere has gases like hydrogen (H₂), methane (CH₄), and ammonia (NH₃) — these are electron-rich gases that tend to give electrons rather than take them.​ ➡️ This kind of atmosphere helps build up molecules (rather than break them down) — which is exactly what you want if you're trying to make organic compounds from scratch.  -​ -​ Urey Miller experiment: mimic early conditions of earth. Atmospheric gasses as simple starting materials to create more complex molecules.lighting, water cycle. -​ Able to take samples and found that 2% carbon that were created were in the form of amino acids, they were able to create enough complex amino acids used in living cells. Still debating if these conditions that would have existed in early earth, some debate about the reducing atmosphere early earth was -​ Having simple carbon nitrogen and oxygen and hydrogen atoms in simple form with an input energy we can create biological molecules that are building blocks of protein and amino acids Early earth -​ Ocean believed to have a similar reducing environment to the atmosphere. still see pockets of this exist on earth =portal back into conditions of what the early ocean must look like = deep sea vents, high temp, high concentration of sulfur that serve as food for bacteria species that exist/ thermophiles. Live off hydrogen sulfide from deep sea vents. -​ Belveined that these vent communities provide info about early life. -​ Chemolithotrophs: different food source , diff electron donors. Use h2S (heavily reduced), to drive synthesis of ATP. -​ Atmosphere has very little O2, the water dissolved in water was being used as a place to dup electrons into in order to reduce water. using any oxygen that exists -​ Archean-proterozoic: Concerned with creating of prokaryotes, evolution of eukaryotes and evolution of multicellularity into plants or animals -​ Transition from prokaryotes > eukaryotes = Great oxygenation event -​ First prokaryotes a lot of were able to derive energy from sunlight(cyanobacteria, very first photosynthetic organisms that existed on earth) -​ Evidence of cyanobacteria dating back to start of life on earth= stromatolites ( cyanobacteria existing at the surface of oceans as biofilms, over water that traps layer sediment) -​ Decline during the cambrian explosion Archean-proterozoic: -​ Cyanobacteria = capable of photosynthesis and evolved the ability to create a very efficient form of photosynthesis which ends with the production of oxygen= Converting early earth that was reducing atmosphere into an oxidising one (rusting of the earth)oxygen -​ As we increase the concentration of o2 were changing the way life utilizes available chemicals= creating the ability for life to be more efficient at generating its own energy. -​ Oxygen intolerant organisms = extinct Great oxygenation event -​ Begins 2.5 billion years ago but we don't see an increase atmospheric oxygen until 850 million years ago= cyanobacteroa -​ Evidence:Banded iron formations where we see abundant between 2.5 and 1.8 billion years ago (production of oxygen) -​ Gap between initial rise of oxygen: transition from anoxygenic photosynthesis ( produces energy for themselves but no o2 as a byproduct) but then shift towards oxygenic photosynthesis -​ Production of O2 got absorbed by the earth first, minerals, ocean chemistry. ( not immediately released into the atmosphere). Oxygen is very reactive, reacting with iron and sulphur to form these rocks = iron formations.  -​ Eventually the ocean and earths crust becomes saturated and there's more molecular oxygen being produced and atmospheric oxygen rises. -​ Evolution within prokaryotic species that became very good utilizing oxygen, for efficient metabolism> ATP -​ Then this is the time we see evolution of eukaryotes: First eukaryotes: -​ Created by endosymbiosis: where early non eukaryotic organisms (archaea and prokaryotes, efficient at capturing sun energy or producing chemical energy through ATP) -​ If archaea you may derive energy by engulfing prokaryotic organisms but you engulf a prokaryote (hudge ATP and capturing sun energy), keep it around rather than completely digesting it , as it provides an internal energy source for archaea. -​ Mitochondria and plastids (double membraned organelle ) were free living bacteria that were engulfed by an archaea, and these make eukaryotic organisms. -​ Evidence: There are prokaryotic cells that have photosystems that are similar to plant photosystems. Prokaryotic cells can exchange genetic material by horizontal gene transfer, getting photosystem 1 and 2 in a prokaryotic isn't hard. -​ Both mitochondria and chloroplasts have DNA that is separate from DNA in nucleus -​ DNA and the genes in the mitochondrial genomes and chloroplast share more similarities to bacterial genomes.(circular, Sequences for ribosomal RNA closer to prokaryotic rRNA than eukaryotic) -​ Replication of these organelles is very similar to replication for prokaryotes( pinching) -​ How eukaryotes came to be , by retaining a cellular battery and food source Paleozoic: cambrian explosion, invasion of land, appearance of gymnosperms, major tetrapods -​ Evolution of first multicellular organisms , animals. -​ Ediacaran fauna: explosion of animal life, rapid evolution of diff animal species. Now extinct -​ Cambrian explosion: additional adaptive radiation, into more life form, evolution.: rapid appearance of the groups of organisms we have currently. -​ Before this: ediacaran fauna to see what sticks. Some things that did stick would provide significant evolutionary advantages like armour (appearance of shells) -​ Evidence for all the diff life forms such as soft body preservations high number -​ Arthropods, echinoderms and a large number of extinct forms -​ Where we start to see lots of body parts that we see to be conserved until now : heads, mouths, eyes and legs.Evolved during this time period -​ Many major animals appeared during the cambrian: explosion of life. -​ Selective pressures on specific genes -​ Explosion of life:genetic diversity present (increasing levels of oxygen ) , and grasing- opening of niches (motuh parts , and eat algal mats), -​ Formation of shells through calcium carbonate Extinctions and mass extinctions -​ Rate of speciation be greater than background extinction , producing more organisms than extinction organisms -​ Mass extinction: ,assive raes of extinction that greatly exceeds rate if speciation (75% of known species) -​ Happens periodically as part of life. -​ Clear ecological niches and make opportunities for adaptive radiations \ speciation -​ Cleaves with very little diversity ,remaining. compared to diverse lineages