Evolution Notes.pdf

8/28 - Biological evolution: phenomenon - How genes change over populations - Evolutionary biology: area of research - Framework for understanding why these phenomena exist - Evolution - Change in the inherited traits of a population that occurs from one...

8/28 - Biological evolution: phenomenon - How genes change over populations - Evolutionary biology: area of research - Framework for understanding why these phenomena exist - Evolution - Change in the inherited traits of a population that occurs from one generation to the next - Variation exists - Genes are inherited - Occurs over time - Traits are selected - Change in allele frequencies, like the moth 9/2: how to study evolution - Homologies - Characteristics that species share through common ancestry - E.g. cetaceans are mammals, like hippos - Phylogenies - Based on homologies, and time of evolution (molecular clock) - E.g. all cetaceans have a dense involucrum (slide) - Synapomorphy: characteristic present in all organisms in a group including the common ancestor AND is absent outside the group - AKA a homology that defines a group/clade - Plesiomorphy: common characteristic between clades that evolved earlier, like amniotic sac between mammals and birds - Connects clades - Isotopes - E.g. O18 is more common than O16 in ocean (both are stable) - SARS-CoV-2 - Had many mutations very fast - When a mutation matters enough and is virulent enough, we call it a variant - If variation in fitness, we expect increase in fitness over time 9/4 - Origin of biology - Aristotle created Scala Naturae - Organisms classified based on form and function - Middle ages and renaissance - Great chain of being: organisms based on theological framework of hierarchy and purpose - Included rocks and fire - Scientific revolution - Copernicus, Galilei, Newton; scientific method - Biologists were called natural theologians  - School of medicine used comparative anatomy, physiology, and embryology; similar across organisms - Developed idea of species (John Ray) - William Paley: the watchmaker - Something that is complex/seemingly impermenant must have a creator - Carolus linnaeus: - Niels Steensen: fossils - Realized shark teeth looked like fossils, so they must be the same thing - Stratigraphy: layers of earth show time - Buffon: earth may be broken off of the sun and cooled down over 80,000 years; populations can change over time over generations - Cuvier: organisms cannot change; fossils must be extinct animals - Mary Ann Anning - Would find and sell fossils, found ichthyosaurus, supported idea of extinction - James Hutton and Willliam Smith - There are slow processes that create mountains, so earth must be much older; maybe animals also change slowly over time - Origin of life - Erasmus Darwin - All warm-blooded animals came from original ancestor - Lamarck - Orthogenesis: constant spontaneous arrival of life, and it became more complex over time - Inheritance of acquired of characteristics - Darwin - Collected birds, ornithologist said they’re all finches, but they have different beaks - Inspired by Malthusian population growth - Logic - Reproductive potential of any organism should lead to exponential growth - However, populations are usually stable, and - Resources are limited and tend to remain constant - Thus - There must be a struggle for existence among the population; and since individuals are not identical and variation is partially heritable, survival is not random (natural selection) - This leads to change in populations - Alfred Wallace came to same conclusion, they published together 9/6 - Presentation tips - Short title, little text - Use figures - Darwin had several ideas not just natural selection - Evolution as it is - Non-constancy of species - Most biologists agree that microevolution occurs in populations, small changes - Just because a species doesnt change over time does not mean A) evolution isn’t happening or B) evolution is disproved - Disproves essentialism (which is the idea that there is an ideal of every thing, there is one perfect lion and the other ones were imperfect variations) - Common descent - Wallace: butterflies in Malay were similar but different, but more similar than they were to butterflies in south america - Today, paleontology (comparative anatomy) and evo-devo (comparative embryology) - Gradualism: microevolution - Opposed saltationism which is like essentialism - Changes are not sudden; e.g. one individual has 3 eyes, then a few more in the next generation, so on - Does not have to be good mutations, can be random mutations that spread; unlike natural selection, which is deterministic - Today is studied through genetics and population genetics - Natural selection - Production of variation and its sorting by selection and elimination - Is deterministic: if an organism has certain traits, you can predict if it will be more successful - This is how it differs from gradualism; natural selection is just a specific deterministic example of gradualism - Multiplication of species - Evolutionary biology, phylogenetics, reproductive isolation - E.g. mockingbird females like songs they heard when they were growing up, one bird travels to another island, doesn’t like song, doesnt mate - speciation - Sexual selection - Not really considered one of the 5 ideas; a component of natural selection - Sexual selection is important in fitness, so it is a component of natural selection - Darwin says it is a different mechanism - 2 types - Male-male competition e.g. bigger antlers to fight another elk, then the bigger one contributes more to next generation - Female mate choice e.g. bird dance (not accepted during Darwin’s time because people didnt think animals had  cognitive processes, and because it implied females influenced evolution of men which people didnt like - Different mechanism because he said “maybe birds sing beautiful songs just because they are beautiful”, this has not been accepted 9/11 Review: - Ortholog: homologous genes in 2 different species but come from common ancestor - Green gene (and blue and red) - Paralog: homologous genes that result from duplication in 1 species that isnt in another that has only 1 copy of the gene - E.g. Blue a and blue b on 1 chromosome in fish are paralogs to each other; both are ohnologs to the single blue gene in fish - Ohnolog: homologous genes resulting from whole genome duplication - Red gene - Glitches in evolution - Constraints while tweaking - E.g. typewriter - If someone typed too fast, it would catch; they held a competition to see which keyboard layout would allow the fastest typing, which was QWERTY - We still have QWERTY on computers even though they are not needed - Things that were tweaked in the past that affect the current - Vagus nerve - Comes down, 1 branch does internal organs and the other innvervates the brain close to where it originates; bad design, gets constrained on the way down - But it evolved a while ago so evolution can’t fix it now Fossils: - Fossil record is incomplete because fossilization is a difficult process - Organisms must die where sediments accumulate, and animals shouldn't eat all of it - Bones are covered by water, sediment comes from down a mountain, fossilize - We use radioactive dating of volcanic ash layers above or below fossils to date fossils - Radioactive decay occurs at a known rate - C-14 half-life 5730 years, why is it not all gone - It is being created by the sun (UV light) - When we die, we do not assimilate more carbon, so no more C-14 - Useful for human remains - Rocks are heterogenous with different minerals, but the rock formed at the same time - Some minerals decay, some don’t - What else can you learn - Behavior - Mating behavior  - Birth - Predation - Function - Like the dinosaur that used its head as a wind instrument - Ecology - Habitat changes - Diets - E.g. seafood vs land plants have different C13/C12 ratios 9/18 - Populations have genetic continuity through time - Phylogeny terms - Tips node branch and clade - Tip: frog and human - Nodes: tetrapod - Internal node: node - External node: tip - Branch: line connecting early vertebrate to tetrapod (series of populations in time) - Clade: tips + most common ancestor node - Quiz question 2 - Time line is wrong, should be vertical pointing down - The timeline should be perpendicular to the tips - New fossil only constrains the youngest age of the common ancestor - Rooted vs unrooted trees - Rooted: shows ancestral to derived timeline - Unrooted: no time information, no derivation information - Taxonomy - Science of classifying organisms - Phylogenies - Characters: like skull - Identifiable heritable traits - Use ancestral and derived, not primitive and advanced - Character state: 0 or 1 for absent or present - I think(???) that characters contain both plesiomorphy and synapomorphy - Synapomorphies: hair and milk for a mammal (define a clade, present only in group) - Monophyletic clade, p SEE SLIDE - Homoplasy - Character state similarity not due to common descent - Like shark and dolphin having similar shape - Principle of parsimony - When organizing a phylogeny, you want the least amount of dots (which show either addition or subtraction of a character) 9/20 - Fish in caves  - Lose eyes, pigmentations - Gain taste buds on skin - Due to developmental regulatory genes - GWAS: genome-wide association study - Look for associations between phenotypes and genes, like height and genes - Phenotypic variation - Reaction norm: range of phenotypes expressed by the genotype along an environmental gradient - Humans and chimpanzees have same genome - Biological differences must be occurring at a different level: regulatory mutations - Mary-Claire King - Military coup in 1970 in Argentina for 8 years dictatorship, made many people disappear and stole newborns, she developed paternity test to find out these kids - DNA - In eukaryotes: chromosomes and histones, diploid - XY sex determination is not the norm across species - Gene expression - A lot of DNA that does not code: either regulates, or transcripted but not translated, or something else - Regulation - Inhibitors that block transcription, or from exiting nucleus, or translation, or post-translation - Pre transcription - Tight winding around histones block polymerase - Transcription - Repressors bind silencer sequences, activators bind enhancers to activate polymerase - Cis and trans regulation?? 9/25 - Get notes from 9/23 - Transposable elements - Retrotransposons: class 1 transposons?? - Will be transcribed, make DNA from RNA, insert DNA from RNA - Some are like viruses (LRT-retrotransposons), others are not (non-LRT-retrotransposons like LINE and SINE, long intermediate nuclear elements, SINEs lost some of these elements so they’re not active anymore) - Class 2 transposons - Just move around the genome - Examples of transposons moving to cause a change - Change maize color, and grapes to turn green, pepper moth - Make up 50% of genome - Only 1.5% of genome codes for protein - Chromosomal inversions  - E.g. Ruff bird has 3 types of males (independent, satellite, and faeder who tricks the male by entering its territory to steal females) - Caused by inversion for faeders, as well as recombination for satellites - Gene duplication - E.g. opsin genes duplicated to sense more colors - Whole genome duplication - E.g. duplication and differentiation of eln gene in fish changed structure of heart - Leads to different things - Mostly leads to loss of function of one of the genes, becomes pseudogene - Some are kept - Neofunctionalization: totally new role, like new opsin - Subfunctionalization: both genes do something similar, complement each other; like the fish heart elna and elnb do different parts of the heart; same overall job is being done but now by 2 genes which allows for specialization - More ploidy causes faster divergence through mutation and faster adaptation, fitness changes faster - But as genome size increases, mutation per base decreases - So as genome increases, DNA repair seems to improve, such that there is a constant rate of total mutation: Drake’s constancy hypothesis - But this is not true in macro eukaryotes, like drosophila and humans mutate way faster (humans 80 mutations per genome) - Most mutations are inherited from father - Only 24 cell division in all ova - Hundreds of mutations in sperm, increases with age - And viruses mutate way way faster 9/30 - Midterm - Directly from slides - E.g. great oxidation vs multicellularity what happened first (oxidation since its necessary for multicellularity); or prokaryotes (cyanobacteria were responsible for releasing oxygen so answer is prokaryotes) - E.g. mary ann what was her contribution - Her findings extinct animals discovered animals existed in the past and they dont anymore so they must be extinct - E.g. synonymous and non synonymous evolution; non synonymous affects protein structure - Dont memorize numbers, understand concept - E.g. why volcanic ash and not sedimentary rock to date fossils - Class - Drift - Drift is always present - Minute q’s  - Synonymous and nonsynonymous substitution has same effect on fitness - We expect to have different effect because nonsynonymous substitution changes structure of proteins so modify function - Synonymous changes gene expression, many of nonsynonymous does same - There is gene and then promotor region - Mutation in promotor region will affect expression - Drakes constancy - Does not hold with eukaryotes for several reasons - Too costly, different generation times, repair mechanisms, somatic vs germline mutations, drift (mutation rate changes with effective population size) - Slides - Hardy weinberg - Assumes a gamete pool of possible haploid gamete combinations of diploid individuals - Allele frequencies - D+H+R=1 - Dominant heterozygous recessive phenotypes - p = D + H/2 - q = R + H/2 - After 1 generation of random mating, you should be able to reach equilibrium, and then allele frequencies should not change from generation to generation - If the 5 assumptions are true - Thus HW theorem is a null hypothesis - 4 mechanisms of evolution: change allele frequencies - Selection - Migration - Mutation - Drift - Due to random processes - Heterozygous genotypes will decrease as one allele becomes fixed; maximum value when p and q are equal - Bigger effect when population size is small