Week 4 Notes
Week 4 Notes GE 70B
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General Education Cluster 80A Frontiers in Human Aging
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ANTH 120 001
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This 6 page Class Notes was uploaded by Sarah Doberneck on Sunday January 31, 2016. The Class Notes belongs to GE 70B at University of California - Los Angeles taught by Dr. Friscia in Winter 2016. Since its upload, it has received 29 views. For similar materials see Evolution of Life and the Cosmos in General at University of California - Los Angeles.
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Date Created: 01/31/16
Locus- a place on a chromosome (often referred to as a gene) like eye color Allele- a particular variant at a given locus, like brown, hazel, blue As diploid organisms, we have homologous pairs of chromosomes For a given locus we have 2 alleles (an entire population may have many more than 2) Central dogma explains how DNA (genotype) carries the information for making proteins (phenotype) Genotypes are inherited. Phenotype star subject to natural selection o Natural selection acts on the proteins (not directly on DNA, but on the expression of DNA) o But it's the change in genotype frequencies over time that defines evolution Evolution must happen at the level of protein coding genes o Thought that Only about 1% of the entire genome that is important in evolution However, gene regulation affect how the protein coding genes are used and when they are used which is almost equally as important Two important points: 1 Phylogenetic trees represent the evolution of species 2 They are built using one or more characters from those species, rather than all of them therefore they are a hypothesis to be tested Trees sometimes are made using just fossils, which makes them rely more on morphology Forelimbs, teeth Life history traits o Particularly useful for invertebrates, where the adult stage of life is often dramatically different from larval states o Limmaeus and get barnacles were mollusk so because they looked similar.. But larval characters were then used to reclassify them as crustaceans Molecular phylogenetics Overwhelming majority of phylogenetics are now reconstructed using DNA sequence data o Ideally more objective o Lots of available data o Capable of resolving both young and old relationships Homologous dna o Homologous characters are defined by common descent o Just as important for DNA sequences as it is for morphology o DNA sequences must be different but not too different Differences are informative. Whole similarities allow alignment of homologous sites Dna sequence alignment o DNA sequences must vary between species because then there's nothing to compare o Can't differ too much though because then it's useless Distance matrix o Number of substitutions (DNA or amino acid) between any two taxa o You can get change sin DNA that don't change entire amino acids made by the protein, so by substituting the DNA for the amino acid and comparing the alignment of that instead there will be less changes Gene trees do not always match species trees o You can map how the gene evolved. But not how the species evolved o The genes move around between individuals of a given species, but only until that population diverges into two species o Notice that some purple dots have no offspring, others have more than one (this is genetic drift and/or selection) Incomplete lineage shortage o Gene trees don't always match the species trees, results in inaccurate information o How is it fixed? Use more than one gene, ideally the correct signal will be more prevalent than the one that are wrong o Use math to model how DNA evolves Use computer programs to detect changes Phylogenomics Entire genomes can provide results with high confidence Very computationally intensive Uses hundreds of thousands of loci because the entire genome is too big Choosing loci o Quickly evolving genes helps us resolve more recent relationships Micro satellite loci are used to look at populations because they are so quickly evolving and will stay in the group you're looking at o Slowly evolving genes help us resolve deep relationships Protein coding genes led to amino acid sequences that allow for cross specie analysis The modern synthesis A grand unifying theory of evolution Synthesized evolutionary ideas of: o Biologists (natural. Selection) o Mathematicians (population genetics) o Paleontologists (fossil record) Evolution is consistent with known genetic mechanisms and the observational evidence of naturalists Evolution is gradual, small changes accumulate over long periods of time Natural selection is by far the main mechanism of change, even slight advantages are important when continued across generations. The strength of natural selection in the wild was now considered greater than previously expected The role of genetic drift is minimal Must think in terms of populations not individuals. Genetic diversity in natural populations is a key factor Extrapolation from micro evolution to macro evolution is proposed Neutral theory Introduced by motoo Kimora 1958 o Contradicted neo Darwinist view of the modern synthesis o Most observed mutation have no effect on fitness o Most DNA is non coding Protein coding genes are broken up into chunks that are non coding (introns) Protein coding exams are often much shorter than the introns that interpret them Silent mutations rule o Changing the third position protein doesn't see like a big deal because you still get the same amino acid so it doesn't seem like a mutation but it is The nature of mutations Enzymes repair DNA damaged by oxidation, uv radiation, etc. They also correct mistakes in the DNA o This is not a perfect process, sometimes mutations aren't repaired and become genetic variants o If it happens during gamete formation, mutations can be passed to offspring Molecular clocks DNA changing without having an effect in phenotype Graph looking at how long it's been since two species were similar Some genes evolve more quickly than others o For example, protein coding genes evolve more quickly in warmer environment Branch length Nodes represent lineage splits, and tips represent extant taxa In a cladogram, the length of branches mean nothing In a phylogram, they represent the amount of evolutionary change (# of DNA substitutions. Indicated by scale bar) Time calibration Turn a phylogram into a Fossils are most commonly used to give an absolute age However, not all species have fossils Using biogeography, you can look at geologic or climatic events that separated populations which led the, to evolve and become distinct species Global cooling o Warm water coastal snail communities Breaking hardy Weinberg equilibrium Selection favors throttles tin the population, I.e. Those that have those offspring Selection. Can be artificial or natural This will change the gene friendliest in the population because the phenotype a that selection acts on are based on genotypes Adaptation The grants have been measuring the finches on the Galápagos Islands for decades A drought hit the island in 1977, and only large seeds were found Within that time, there was a change in the average beak sizes o There was a variation in beak size o More individuals were produced than could survive o That variation elated to survival o The variation was heritable Industrial melanin in the peppered moth Moths come in light or dark shades In the late 1800s they measured a spread of the dark forms, amount of dark increased Culturally, this was the industrial revolution meaning a lot of coal was being burned and releasing that pollution in the air o Killed the lighter, greener things on trees and rocks o Soot collected on the trees o No the dark form was much better camouflaged because the trees had soot and lacked miss Bernard kettle wall tested the pollution hypothesis and found strong support for the impact of moth color on susceptibility to bird predation In 1958, the uk passes the clean air act, resulting in less pollutants o Looked at the moths again, found there were fewer and fewer of the dark forms as the likins returned 1963 the us passes their own clean air act o Looking at a moth in Michigan similar to the English one, also found an almost exact change in the amount of dark moths that went away while light months increased Malaria History of the evolution of DDT resistance o Spread a whole bunch of DDT to kill off malaria because they knew it would kill it o After this, the number of people affected with malaria went down by a lot o However, about half a century later, it was back with just as many people affected By 1970 the mortality rate of mosquitos was a fifth of what it was at first even with ten times the dose They evolved a resistance to ddt All 4 premises are met o Mosquitos vary in resistance o They reproduce and more are produced than survive. They are subject to selection in the form of didn't poisoning o Vary in character that affects resistance o Resistant mosquitos live and pass on that trait Clearly, there are limits to the power of selection and structures ar produced that are less than ideal Constraints imposed under phylogenetic history. Evolution builds on what is there. We are descended from a quadrupedal ancestor, so some aspects of our anatomy such as our backs, knees, and feet are adequate but often fail Lack of appropriate amount of genetic variation Natural selection can't act on traits that appear post reproductively. The deleterious genes have already been passed onto the next generation Developmental interactions among organs or structures that necessitate trade offs. For example, having larger babies might compromise female pelvic and hip structure Modes of selection Directional. One extreme phenotype is the most fit Stabilizing. An intermediate phenotype is the most fit Diversifying. Two or more phenotype are more got than the intermediates between them Selection can act of multiple traits creating an adaptive landscape Different modes of selection exhibit different departures from hardy Weinberg equilibrium Directional o More with AA survive , so you get more homozygous and excess dominate Excess heterozygosity Excess homozygosity Example of balancing selection: sickle cell hemoglobin One allele in the beta-hemoglobin locus encodes sickle cell hemoglobin o This carries oxygen led effectively o Red blood cells adopt a sickle shape and break down easily In the absence of malaria, AA homozygous have the highest fitness o sS homozygous have severe Armenia and usually die before reproducing o AS heterozygous survive In areas we here malaria is common, heterozygous have the highest fitness o SS homozygous have severe Armenia, die before reproducing o AS heterozygous, have slight anemia and some malaria resistance o AA homozygous have high mortality rates from malaria S allele has aligned frequency where malaria is common Another example of selection in humans: lactose persistence Humans normally lose the ability to process lactose as they grow In populations that domesticated cows early on, there has been selection for a persistence of the lactose producing ability Genes following the selective gradient here Drift and selection tend to be in opposition of each other Whichever wins depends on the population size Adaptation Bacteria example o The broth medium that the bacteria were gown in container a compound called citrate o Normally they can't process citrate in an aerobic environment, but eventually they were able to o A duplication in the gene allowed this to happen Gene duplication is often the tool for adaptation Evolution is a tinkerer, doesn't make new material but uses what is already there The gene tree allows us to see these evolution of these changes o Example.. Beta defensin are usually used for fighting off bacteria in vertebrates. Eventually, snakes used this in their venom HIX genes Set up are of body orientation Where to get arms legs head Highly conserved, works the same way in the exact same genes across many species Humans have the Same HIX genes compared to flies Duplicate events through evolution mean we have more than flies do Limb axes o Axes are determined on the limbs in a similar manner to the axes for the entire body Evolutionary axis A fish limb develops very differently the a vertebrate limb o Fish are very symmetrical, we are not Polydactyly o Extra limbs o Happens went the gene for making like a finger or something didn't turn off at the same time Flippers o Extra bones in their limbs
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