Week 6 Notes
Week 6 Notes 82669 - BIOL 3350 - 001
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This 11 page Class Notes was uploaded by Abigail Towe on Tuesday September 29, 2015. The Class Notes belongs to 82669 - BIOL 3350 - 001 at Clemson University taught by Lisa G Rapaport in Fall 2015. Since its upload, it has received 12 views. For similar materials see Evolutionary Biology in Biological Sciences at Clemson University.
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Date Created: 09/29/15
Population Genetics What is evolution Evolution is the change in allele frequencies over time How do we know whether allele frequencies are changing calculate the relative frequencies of each genotype within a population I Estimating allele frequencies A Calculating observed relative frequencies of each genotype within a population 0 Examine a single trait coded by a single gene with 2 codominant alleles 0 Example Four O Clocks 0 Observed phenotypegenotype relative frequencies the same due to codominance single gene trait with two codominant alleles 0 P relative frequency of A1A1 genotype of A1A1 individualstotal number of individuals in population 0 H relative frequency of A1A2 genotype number of A1A2 individuals total number of individuals in population 0 Q relative frequency of AZAZ genotype number of A2A2 individuals total number of individuals in population AlAl A1A2 A2A2 P H Q 0 Observed allele relative frequencies 0 of A1 allele p P 12H O of A2 allele q Q 12H 0 These are relative frequencies so p q 10 0 Example in a sample of 1000 individuals from a larger population the follow number of individuals of each genotype were observed 0 What s the relative observed frequencies of the A1 and A2 alleles in this population Genotype N Relative Frequency of alleles P AlAl 240 P 12 H 44 H A1A2 400 Q A2A2 360 Q 12 H 56 p A1 P 12 H 240 2001ooo 44 q A2 Q 12 H 3602001000O56 ll HardyWeinberg Equilibrium HWE A When no forces of evolution influence allele frequencies at a single gene locus 1 Consequences all about stasis o loci is said to be in genetic equilibrium 0 genotype frequencies will remain the SAME from to generation 0 HWE is a property of a GENE not of an individual or a population It basically allows us to test if evolutionary change is occurring 2 Assumptions of HWE 0 large population size N gt 1000 0 this insures no effects of genetic drift 0 when population is very small then just by chance the frequency of alleles might vary widely o it assumes that there are no external forces pushing genotypes frequencies in one direction over another no natural selection no mutation no migration 0 it assumes there is random mating with respect to genotypes no assortative mating no sexual selection and no inbreeding o if all of these conditions are met it will be possible to predict the frequency of alleles in a population 3 Are these assumptions ever met Yes but must be selectively neutral loci o selectively neutral loci genes whose phenotypes have no positive or negative effects 0 Example blood cell surface antigens 0 antigens like LIVI LN or A B 0 blood groups HWE assumptions met 0 human population is large 0 mutation is so rare as to be negligible 0 no selective advantage to these alleles o mating is random with respect to blood type 4 Formula to predict expected frequencies Derived from gamete frequencies p2 2pq q2 10 If a locus is in HWE one can use the following formula to predict the genotype frequencies from the allele frequencies p2 2pq q2 10 Where p2 relative frequencies of A1A1 2pq relative frequencies for A1A2 heterozygous q2 relative frequencies of A2A2 B Implications of HWE for a gene locus 1 What does HWE predict with regard to gene frequencies across generations 0 genotype frequencies will remain constant from one generation to the next 2 What does HWE predict with regard to allelic frequencies across generations 0 allelic variation is NOT LOST between successive generations 0 Even if one of the alleles is rare 0 they won t go extinct if locus is in HWE 0 thus most ofthe A2 alleles are found in heterozygotes and will be maintained as long as the locus remains in HWE 3 How fast can a locus reach HWE in a population 0 simply ONE generation of random mating will restore a locus to HWE 4 Single locus with multiple alleles can also be in HWE o 3alelespqrquot2 c or pquot2 2pq rquot2 2pr 2rq qquot2 10 5 Sexlinked loci can be in HWE 0 femalespquot2P2pqHqquot2O 0 males p P and qQ C Using HardyWeinberg Equilibrium as a test for evolution 1 What does HWE predict with regard to gene frequencies across generations 0 HWE predicts that the allele frequencies will remain the same across generations 2 What is evolution in genetic terms 0 evolution is a change in allele frequencies across generations 3 What do deviations of observed genotype from expected frequencies tell you 0 thus deviations of observed genotype frequencies from expected HWE genotypic frequencies EVOLUTION at that locus 4 Example is our observed frequency of alleles what is expected if not the evolution is occurring PA1A1 240 024 p2 P2 044gt2 019 2pq 2pq 2O44056 HA1A2 400 040 049 QA2A2 360 036 q2 q2 56 2 31 Expected p2 2pq q2 10 What we really want to know 0 Do OBSERVED genotype frequencies EXPECTED genotype frequencies o P pquot2 24 19 o H 2pq 40 49 0 Q qquot2 36 32 No more observed homozygotes and fewer heterozygotes than HWE predicts thus some type of evolution is occurring at this locus What we want to know is Is Pp2 H2pq Qq2 5 Is the difference due to chance 0 Chisqua re test tests if this difference is significant 0 Convert frequencies back to of individuals by multiplying expected value by population size 0 df k r k of phenotypes r of alleles 0 nourcase321df o 240 190219o 400 490249o 360 3202320 1316 1653 50 3469 0 x2 1 df P lt 005 3841 3469 gt 3841 thus reject Ho Evolution is occurring at this locus 2 2 x z0 E IE 0 chi square answers does the number of individuals different in each category differs from the number you would expect 6 Importance of HardyWeinberg Principle to population genetics 0 provides a starting point to test for evolution within populations 0 if locus is not in HWE then evolution must be acting on the locus 0 next step is to figure out which force of evolution is causing the deviation from HWE 7 Deafness in dalmatians 0 Assume HWE with a deafness frequency of 3 what is the frequency of carriers 0 Deafness is a recessive trait found in dalmatians 0 within the US population the frequency of deaf dalmatians is 3 0 assuming that the deafness locus is in HWE what proportion of carriers of this trait are found in the US population 0 because it s recessive to be a carrier you would have to be heterozygous Producing Genetic Variation ll Genetic Mutations Chromosomal mutations 0 Gene Duplications Chromosomal mutations 0 Gene Duplications O O O unequal crossing over a piece of a chromosome is duplicated during crossing over can involve one or multiple genes caused by replication errors something gets copied twice 0 How do they occur 1 3 4 5 homologous don t pair properly so after crossing over one chromosome has a deletion and the other has a duplication occurs rather easily if DNA contains many tandemly repeated nucleotides or genes microsatellites often the new gene is not functional pseudogene orthologous genes new functional gene with same or similar function paralogous new genes that has diverged in function 0 Why are these errors important 0 thought to be important mechanism in the evolution of multigene families I Example Hemoglobin gene family 0 paralogous genes and pseudogenes 0 Example Orthologous gene duplication in humans 0 positive selection for gene duplication in Humans the salivary amylase gene AMYl codes for amylase the enzyme responsible for starch hydrolysis more AMYl genes 9 more amylase produced chimpanzees have 2 AMYl copies humans have up to 18 copies I the number of amy1 genes varies across individuals in humans I more amylase genes in individuals whose diet has been traditionally high in starch positive selective pressure on orthologous amylase genes likely increased after advent of agriculture 510000 yea rs ago 0 Example Evolution of color vision in primates article 0 The evolution of trichromatic color vision in primates primate trichromacy probably evolved in fruiteating primates rainforest fruits and new leaves are often yellow red purple and orange O dichromats have low sensitivity to color differences in the red yellow and green regions of the visual spectrum so how might this evolution toward trichromatic color vision have evolved originally scientists thought that the last common ancestor of the Old World primates and New World primates monkeys were dichromates Therefore it would have to had independent evolution oftrichromacy from a dichromatic ancestor for old world primates the color vision is found on X chromosome 2 genes for color but for the new world the color vision is found on X chromosome but with 3 alleles o if you are a male you can t be heterozygoustrichromatic because it s only on X chromosome so males only have one allele 0 females can have two alleles So when did trichromacy evolve according to the LCA dichromat hypothesis 0 After the New world monkeyold world monkey split late Eocene 35 million years ago Evidence for Early Trichromatic Color Vision jacobs and Nathans 2009 believe that trichromacy evolved well before new world monkey split from old world monkey lineage evidence amino acid sequences in the L and M pigments of new world and old world monkeys are identical unlikely if they had evolved independently through convergence 3 alleles 3 different possibilities 0 but through mutation a duplication could occur you could have 2 genes of the same allele on the same chromosome so now all females and all males can have trichromacy so you go from an ancestor with 3 different alleles to a old world system where basically everyone has trichromacy chromosome conclusion the LCA last common ancestorprobably had an MWSLWS gene on chromosome X with at least two different alleles as in modern New World monkeys after the split an error in recombination resulted in gene duplication event what had been 2 alleles were now two different genes on a single X chromosome this new configuration was favored because all females and males would then have trichromatic vision Jacobs and Nathans didn t talk about this but some people have argued if trichromatic vision is so great then why haven t new world monkeys evolved the same situation that would be highly favorable where all would have it makes researchers think that there is an advantage of being dichromatic o the advantage would be it s easier to see camouflage of prey with dichromatic vision 0 because primates don t just eat fruit they eat insects and frogs that are highly camouflaged 0 The chromatics are much faster at foraging for insects and frogs that are camouflaged also in humans dichromacy in males is more common than expected could have helpedhelps men with hunting V Measuring Genetic Variation A Natural populations 1 Evidence of genetic variation i classic view natural populations harbor very little genetic variation ii since mid19605 natural populations have been shown to harbor enormous amounts of genetic variation 0 Allozyme heterozygosities show high levels of variability 0 if we look at enzymes and look at how many alleles are present in certain gene that codes for enzymes The graphs from the powerpoint show that the variability among invertebrates plants and vertebrates is in great amounts B Determining genotypes o Scoring protein size or nucleotide size of alleles 0 Gel electrophoresis proteins and DNA are negatively charged bands move from negative to positive charges within the electrophoresis ring smaller sizes move more quickly proteins and DNA are placed in negative wells they travel toward the positive end of the gel 0 Polymerase chain reaction can also look at size of alleles a microsatellite is flanked with fluorescent PCR primers amplification will give a series of fluorescent allelic products that will vary in size according to their repeat length a population might possess 5 alleles which vary in size the gel is used to compare microsatellite fragment sizes resulting from the amplification sample 225 is a hybrid based on having two bands 2 differently sized fragments compared to one band in parental species 0 has double band u m Fl I P velif39era IN P mexicam I39m P irmom no I tellem I l nwxictum loo 1 fhrmom quot MP 225 c o N N 0 N e Z 2 Q 2 C 39C Is IU MP 2 o allelic diversity among mountain lion populations in Idaho 0 mountain lions I travel large distances I rarely seen very cryptic and active when we are not ac ve I trying to monitor them is very difficult I There was a study that wanted to determine how healthy mountain lions are in Idaho how they f3 f fquot e x ranged what was the population dynamics in order 39 ZiflvaCEE x K to better understand how to manage them inef vr 3 X 5 I so they amplified loci and each had about 10 alleles sizaagws xquot a equot so it provided a lot of information Nth 117 NEVADA UTAH I they found that the northern and southern population had really different alleles at this locus a Distribution of alleles at FCA 262 lot more diversity in the southern part of the range and southern compared to northern look really different I the snake river is a barrier to these animals they don t swim 0 Alaskan sled dog genetics 0 the allelic diversity in dogs I started as human genome project one of the researchers wanted to explore genome of dogs she was a sled racer I sled dogs used to be used for transportation near polar regions I but now sled dogs are either breed for long distance endurance competition OR they are bred for speed So either endurance or speed I endurancedistance runners have a larger amount of diversity on the genome than the speed runners I distancebred dogs are more genetically different from one another than are those dogs that are bred for sprint racing I distance dogs can be identified by kennel of origin 0 How are these methods used 0 Speciation O Clinal variation 0 Dog breed identification 0 Microsatellite and minisatellite DNA 0 top microsatellite repeats 16 bp repeats shorter total length 0 bottom minisatellite repeats longer total length Repeat units Homogeneous array Heterogeneous array A I r lt 139 Array II gt 7 o A DNA fingerprinting minisatellite usually 1060 bp repeats used to ID crime suspects and determine parentage Helps to determine if suspect s sample matches the bloodstain found at the scene of a crime 0 high degree of accuracy 0 Paternity testing for humans but also a lot of field tests are using it to determine l urcntugc among cohrculingI mulequot parentage of usllings BM m t g 3 g 4 o to look at surVIval and reproduction count babies for females quot quot quot39 quotquot 0 but for males you can look at copulations when female was likely quot 39 to be fertile proxy measures but now researchers can actually look at the heritage of wild animals 0 you look at the minisatellite markers of the genome of the animals look at females babies and the possible fathers 0 however some females aren t actually the moms don t have all the same lines because some females lay eggs in other nests 0 but you can compare the fathers to find the male that has the same markers as specific babies if mom doesn t have the maker for a child you can look for the male that does have the marker to explain where the child got this allele if mom has it then it s not very helpful to determine father gt 0 Speciation especially with regard to cryptic species 0 Example shovelnosed salamanders fully aquatic and thus isolated among different river drainages two distinct species recognized on either side of the Continental Divide analysis of mitochondrial DNA VI Genotype by Environment Interactions A Phenotypic Plasticity a individuals with the same genotype may have different phenotypes i responses to developing in different environments b individuals with the different genotypes may have same phenotype i sensitivity to different environments may depend on genetic variability 0 Example Tobacco Hookworm varying sensitivity to temperature extremes during development 0 variation typically green but sometimes black some are black unless exposed to high temperatures 42C before molting in that case green if not exposed to that high temp then they remain black 0 artificial selection of 3 lines 0 most sensitive to heat 0 least sensitive to heat 0 random control With each temperature they bred two of the same lines to determine offspring resulting color right before molting they would hit with the temperatures 0 12 generations 0 results some black some turned green light green 0 low plasticity line black at all temperatures 0 color of high plasticity line dependent on temperature more likely to turn green at lower temperatures such as 33C than unselected line 42C 0 phenotypic plasticity is adaptive in variable environments
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