Evolution Exam 2 PDF

Evolution Exam 2 Lecture 1 Slides 3 ➔ Evolution affects a population (species) not just an individual ◆ Even though natural selection is working on individuals ➔ Evolution is sometimes short-sighted ◆ Individual care about what's best for them - not for the population/evo...

Evolution Exam 2 Lecture 1 Slides 3 ➔ Evolution affects a population (species) not just an individual ◆ Even though natural selection is working on individuals ➔ Evolution is sometimes short-sighted ◆ Individual care about what's best for them - not for the population/evolution ➔ Evolution works on pre-existing genetic traits ◆ They must already be in the population – they don't develop because you need them ➔ Looking at beak depth, the smaller beaks were selected against, which allowed the finches to all have big beaks ➔ Evolution can not predict the future ➔ Sometimes characteristics already exist and can acquire a new function because of selection – these are a pre-adaptation → work on variation that already exists ➔ In the giant panda, it has a pre-adaptation that allows for better grasping of bamboo ◆ There is a modification in its sesamoid bone that allows the animal to clamp stalk ➔ Infanticide occurs in lion populations ◆ A male lion kills another males cubs that are from another pride, which causes the female to go into heat and reproduce with that male ◆ She wants more offspring ➔ The longer the gonopodia (in fish) → the more likely you are to find a mate ◆ It is easier to catch fish and consume them if they have a longer gonopodia ◆ The fish has two selective pressures occurring at the same time ◆ Longer → better fitness → less survival ➔ Darwin's questions ◆ Thomas Hunt Morgan - Mutation was identified and figured out the genetics behind mutations, realized it was unlimited ◆ Mendel - Variation is passed down to offspring and figured out how – independent assortments and the law of segregation occur ◆ Lord Kelvin – The earth is much older then we thought ➔ Modern synthesis - merge of genetics and evolution 1. mutations, segregation, and independent assortment allows for variation 2. Variation is heritable - alleles are passed down 3. Some are more successful at reproducing + surviving 4. Best allelic combinations survive + reproduce ➔ Evolution was still not fully accepted in 1920s-1960s ➔ Butler act → the law that evolution can't be taught in schools ◆ In 1968 evolution was allowed to be introduces ◆ In 1987 creationism was removed from schools ◆ In 2005 recognition of gaps in evolution ➔ Intelligent design theory - replaced second creation ◆ The presence of a designer that creates perfection of adaptation of contemporary animals ➔ Evolution is a predicted idea  ➔ Goes against Law of thermodynamics Slides 4 ➔ Mutations are not all bad – some beneficial ➔ In the melanistic zebra – mutation in transport protein that is supposed to move the pigment where it is supposed to be ➔ Giraffe has leucism – only the skin cells have no pigment - all other cells are fine ➔ Evolution needs to have a genetic variation - Variation is the raw material that evolution works on ➔ Places we get variation 1. Mutations → one of the ultimate sources of variation 2. Meiosis → creates new combinations of alleles - by crossing over and independent assortment - Genes are found on specific parts of DNA - Genes are recipe for protein, if we have a different allele → different protein ➔ DNA has a sugar phosphate backbone ◆ A + T pair (2 H bond) ◆ C + G pair (3 H bond) ◆ 4 different nitrogenous bases Purines - A + G Pyrimidines - C + T ◆ Phosphodiester bond links them together ◆ DNA → mRNA → Protein ◆ If a mutation changes the amino acid, you might see the effect ➔ Watson and Crick stole Rosalind Franklin’s lab and discovered DNA ➔ Kornberg figured out how does DNA replicate ➔ Mutations are changes in the DNA that can lead to a new protein product ◆ One of the earliest mutations identified has a mutation is hemoglobin that could cause sickle cell anemia ◆ One base change causes the cells to be sickled Lecture 2 Slides 4 DNA → mRNA → Protein Transcription - translation ➔ One of the fist genetic conditions identified was huntington's disease ➔ Another molecular disease studied is sickle cell anemia ➔ Linus Pauling thought that individuals with sickle cell anemia had a mutation that affected the molecular structure of hemoglobin ➔ Vernon Ingram recognized that there was a mutation in the 6th amino acid of hemoglobin, valine was inserted instead of glutamic acid ➔ They found out there was only one point mutation (base change) that led to sickle cell anemia ➔ Point mutations can exist in two types → transitions + transversions  ◆ Transitions swap a purine for a purine, or a pyrimidine for a pyrimidine Create less problems for DNA, and are more likely to persist to the next generation ◆ Transversions swap a purine for a pyrimidine Causes more disruption in DNA structure More likely to be repaired ➔ Genetic code is conserved ➔ 3 base pairs create our codon, which determines which amino acid incorporated ➔ A change in base 1 or 2 is less likely to be tolerated then a change in base 3, because of the wobble effect (third base changes and encodes similar amino acid) ➔ Mutations can be nonsynonomous or synonymous ◆ Nonsynonomous (replacement substitution) will result in the change of the amino acid sequence of the protein ◆ Synonymous (silent mutations) will result in no change in the amino acid sequence – often result from wobble effect ➔ Mutation rate – DNA polymerase makes 1 error per 100 million base pairs ➔ They realized that looking only at phenotypic mutations is not the best way ➔ C. Elegans ◆ Observed them at different time points ◆ Allowed them to replicate 280, 350, 390 times → they put a lot of time into studying this and looked at 390 generations to see how many mutations accumulate ◆ Nuclear DNA has about 2.1 mutations in their genome each time they replicated ◆ Most mutations are INDL – they’re a one base mutation (insertion/deletion/base change) ◆ Mitochondrial DNA had a high mutation rate compared to nuclear DNA Mitochondria is best at looking at mutations since there is a lot of variation Mitochondrial DNA does not have repair mechanisms - more mutations accumulate Mutation rate depends on ◆ DNA synthesis (DNA polymerase) ◆ DNA repair mechanisms ➔ DNA polymerase creates polymers of DNA ◆ By studying DNA polymerase: they found the quicker the DNA polymerase works, the more quickly the genome accumulates mutations ◆ Slower DNA polymerase, the more efficient ➔ Repair mechanisms ◆ The more mutations in repair mechanisms, the higher rate of mutations occur ◆ Familial cancers are inherited and associated with double stranded DNA repairs Mutation Rate ➔ Advantageous when organisms are adapting to new environments or when the environment is undergoing rapid changes ◆ The quicker the mutation rate → can cause a decline in fitness if there is no natural selection  ◆ If mutation is created and not selected FOR or AGAINST -> the populations fitness will decline ◆ The deleterious mutations will accumulate and eventually be bad for the population and the population will eventually die ◆ Selection is very good at deleting harmful mutations → positive thing ◆ Original → continue to make mutations and makes a significant change ◆ Selection gets rid of deleterious mutations ➔ Gene evolution - gene duplication is an important source for evolution 1. Retrotransposition of mRNA (mrna is reverse transcribed to form DNA which is incorporated into the genome - can create pseudogenes OR the gene can be inserted back into DNA and is put under the control of another promoter + can act as a functional gene) - When reverse transcribed they have no introns and no regulatory regions - Fgf4 retro-duplicated gene gives welsh corgis their long legs 2. Unequal crossing over during meiosis also creates gene duplication - When we have crossing over – at non homologous points - If we have unequal crossing over -> leads to gene deletion + duplication ➔ The fate of the duplicate genes ◆ It can maintain the same function -> becomes a redundant gene ◆ It can acquire a neutral mutation (wobble effect) ◆ Gene can acquire a new function (neofunctionalization) ◆ Loss of function (mutation that’s acquired or a truncation – only part of mutation is acquired) (mutation where there's a stop codon in early in the gene) ➔ Globin gene family ◆ Found in two clusters on genome ◆ Alpha is on chromosome 16 ◆ Beta is on chromosome 11 ◆ Hemoglobin is a tetramer made of four subunits (2 alpha + 2 beta) ◆ Throughout development we express different forms of hemoglobin Embryonically - during the first trimester of development - we have specific hemoglobin genes expressed (zeta + epsilon) After 1st trimester - a different combination of hemoglobin is expressed (alpha and gamma) At birth - you express alpha + beta ◆ Gene duplication is also gene in rRNA (ribosomal DNA) - rRNA is randomly placed throughout our genome - has many backups ◆ Find another instance of gene duplications - one in humans ➔ Gene Duplications do have homologous features divided into two types of homologies ◆ Paralogous - similar functions, but not the exact same function - hemoglobin and myoglobin gene ◆ Orthologous - genes in different organisms that come from a single ancestor and maintain the same function throughout evolution ➔ Chromosomal mutations create variation  ◆ Inversions - often created from radiation – get a double stranded break in chromosomes - the fragment that broke off flips and reverses orientation - reattaches in the opposite orientation, which created inverted segment in chromosome Inversions are less likely to cross over Creates a genetic linkage that makes it more likely for the genes to assort together during meiosis ○ Closer together - the less likely to cross over Supergenes are a part of the inversion ○ Heterozygous chromosome – no crossing over Two different chromosomes - sequences don't align homologously like they should - do not cross over Lecture 3 Polymorphic chromosomes → many forms of the chromosome ○ Do these different forms of chromosomes have different frequencies that depend on their climate and location Cline → a change in the allele frequency or inversion over a geographic area ○ Do clines exist in the inversions? ○ After studying the chromosomes, they found that there is selective pressures for the clines - there are different inversions in different geographic areas ○ The body size of fruit flies is climate dependent ◆ Hotter environments - smaller body ◆ Colder environments - larger body ◆ Leads to the creation of a supergene - which is the DNA inside between the inversion Thursday Lecture ➔ Evolution works on… DNA to create variation in our genome ➔ Genome duplication – the entire chromosome set (genome) is duplicated - we have extra copies of chromosomes ◆ Chromosomes fail to separate during meiosis 1 or sister chromatids do not separate during meiosis 2 -> creates polyploidy - more than 2 sets of chromosomes ◆ Gametes have double the number of chromosomes ◆ Works in hermaphrodites and parthenogenetic organisms ◆ If mating with same # of chromosomes the gamete contribution to the next generator ◆ Genome duplication can lead to speciation ◆ If a diploid + tetraploid organisms mate - the offspring becomes triploid Triploid now has a low survival rate Gametes do not form properly ◆ Plants are full of polyploids ◆ Angiosperms are one of the most diverse plants Genome duplication → diversity Genetic Variation ➔ To measure Genetic Variation we look at the alleles ➔ Wild type allele is the most common allele in the population -> have the highest fitness ➔ Mutant allele is less common - any allele that is different from the wild type ◆ Some mutant alleles are better ➔ We look at allele frequency - determine the genotype of a large sample of individuals and look at their alleles ➔ Allele frequency = # of alleles of interest / total # of alleles ➔ Each gene has 2 alleles ◆ Wild type homozygous has 2 wild type alleles ◆ Heterozygous has 1 wild type and 1 mutant alleles ◆ Homozygous has 2 mutant alleles ➔ CCR5 - allows ??????? ◆ To look at CCR5 - extract DNA from cells, use PCR to replicate the DNA and have enough to analyze, once we have DNA - use a restriction enzyme to cut the DNA at a specific DNA sequence, the mutant and wild type have different fragments ➔ Only one individual was homozygous mutated ➔ After studying the diversity of CCR5 in various populations ◆ They only saw it in europe ➔ Statistical summaries of Gene variation in population ◆ Mean heterozygosity: fraction of gene loci that are heterozygous in the genotype of the average individual ◆ Average individual has about 4-15% of gene heterozygosity ◆ Percentage of polymorphic genes: the fraction of genes in a population that have at least two alleles ◆ 50% of genes are polymorphic ➔ CFTR receptor is mutated in individuals with cystic fibrosis ◆ Lines GI and respiratory tract ◆ When a CFTR receptor mutates - we have issues with the mucus membranes ➔ After looking at mutations they realized there are 500 different mutations that lead to a mutated CFTR receptor Slides 5 ➔ There are important life stages for population genetics ➔ We look at gametes which combine to create a zygote, the zygote develops into juveniles 10/15 ➔ Hardy weinberg equilibrium - p2+2pq+q2 = 1 ◆ Going against HWE - we see evolution ◆ Gives direction on how to study evolution ➔ NO - mutation - drift - selection - migration, & huge population ➔ Punnet square sperm * egg = zygote ➔ Selection in minimal amounts can cause a change ➔ Food spiked with ethanol - developed more Adh F (alcohol breakdown) ➔ Kuru ◆ In females - consumed x ➔ Malaria ◆ Placental inflammation - nourishing baby ◆ Selection ➔ CCR5 mutation - ➔ If selection is affecting dom vs recess alleles ◆ If dom is lethal - wiped out in one generation ◆ Recessive will continue to persist ➔ Sterilization statue ➔ Lethal dominant → all die - selection kills all of them ◆ Sporadic mutation → will be wiped out – wont create more variation in population ➔ Heterozygous superiority (overdominance) ◆ The heterozygous form is more fit then either of the homozygous forms ➔ Underdominance ◆ The heterozygous form is lethal ➔ Overtime if heterozygous is more beneficial we will see a change in allele frequency ◆ Can happen from health complications or selection of mates (hetero is selected for) ➔ Eugenic sterilization – Feeblemindedness - they tried to sterilize individuals who they thought were feebleminded ◆ Over 250 years, there was a slight allele frequency change ◆ By trying to sterilize population - you will not see a lot of change ➔ Mutation is a weak mechanism of evolution - slow effects ◆ Mutation is the raw material for evolution to work on ◆ Mutation creates slightly different alleles ◆ Barely creates change in genetic material ➔ E.Coli - study bacteria to see mutations ◆ Bacteria since it replicates so fast ◆ No conjugation - can only change through mutation ◆ Accumulate one mutation in populations over 10,000 generations ➔ Looked at 3 generations of E.Coli -> allowed for selection and mutation to accur in their population ◆ Cell size increased when having selection and mutation ◆ They stopped the ability for selection, allowed the population to accumulate just mutations, and saw no changes in the cell size ◆ Selection helps cause a significant change, while just mutation does not play a significant role ➔ Mutation selection balance ◆ Mutations are created and selection will eliminate deleterious mutations from the population, but these mutations are constantly created → creates a mutation selection balance  ◆ The rate at which copies of deleterious alleles are eliminated by selection = the rate which new copies are created by mutations in allele frequencies and are at equilibrium ◆ Creating mutations and selection against them at the same rate - creates equilibrium → doesnt increase or decrease in rate - just persists ➔ Spinal muscular atrophy ◆ A neurodegenerative disease that causes wasting and weakening of muscles ◆ On chromosome 5 – mutation in telSMN gene (dont memorize) ◆ Second most lethal autosomal recessive disease - (1st is cystic fibrosis) ◆ Condition still occurs because of mutation selection balance - still prevalent but no selection for it ◆ Mutation that is created and selected against when resulting in a deleterious mutation ➔ Cystic fibrosis ◆ Most common mutation studies ◆ 4% of the population are carriers for a CFTR mutation ◆ Mutation on chromosome 7 ◆ Autosomal mutation ◆ Used to die young, but our new treatments have prolonged life ◆ They wanted to find out - is mutation selection balanced or does it have heterozygous superiority?? – it has heterozygous superiority ◆ There are certain times where having mutation is beneficial ◆ Being a carrier makes you less susceptible to having typhoid fever ➔ Typhoid fever is a bacterial intestinal infection that enters the body through CFTR receptors ◆ If we do not have a mutation in CFTR receptor - you become more ill and can die ➔ Mice study - Created mutation in mice ◆ Compared homozygous wild type mice vs heterozygous (most common) vs homozygous mutant ◆ If you have wild type - the bacteria enters through CFTR more easily ◆ If you are homozygous mutant - less likely ➔ They looked at populations where typhoid fever was an issue ◆ They saw that after typhoid fever - there was an increase in CFTR mutations ◆ Looking at generation - mutations persisted