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week 9 of notes

by: Katelyn Scott

week 9 of notes BIOL-L 105

Katelyn Scott
GPA 3.0
Introduction to Biology
T.J. Sullivan

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this is the 9th week of notes
Introduction to Biology
T.J. Sullivan
Class Notes
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This 29 page Class Notes was uploaded by Katelyn Scott on Friday September 11, 2015. The Class Notes belongs to BIOL-L 105 at Indiana University taught by T.J. Sullivan in Summer 2015. Since its upload, it has received 18 views. For similar materials see Introduction to Biology in Biology at Indiana University.


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Date Created: 09/11/15
103114 E 43 CH MRSA MRSA I MRSA methicillin resistant Staphylococcus aureus Genetic variation environmental variation gt variation in reproductive success between genotypes Staphinfections I Antibiotic methicillin was used to start treating infections in 1959 103114 103114 Natural selection MRSA I Methicillin resistant bacteria found in the UK in 1961 Frequency l l l I no 200 400 sun 300 Toughness 103114 103114 103114 47 I MRSA I Tuberculosis 2 W c 30 5 8396 31 a gt g 8 g ITB 0 3 E 5 2 Mycobactenum 3 3 Z Vancomycin tuberculosis K 0 o a resustant r Vi 1r 3 5 10 Vancomycin use S aureus Sp ead a a E 2 begins here Respiratory infection g g cough chest pain a fever etc o T V l T I l 1975 1980 1985 1990 1995 2000 2005 N W Year Tuberculosis Tuberculosis 392 types 0f mfectlon I 13 of the world s population is infected TB disease I Express symptoms of the disease l9 million had full disease in 2010 Latent infection 14 million deaths I Get exposed by immune SYStem keeps the ILeadin cause of death for eo 1e with HIV infection in check can convert to TB disease g p p 103114 No of Cases Reported TB Cases United States 19822010 30000 r 25000 20000 939 O O O Updated as ofjuly 212011 TB Case Rates United States 2010 Cl 5 36 2010 national average gt36 Cases per 100000 Drugresistant TB ITreatment requires antibiotics ie rifampin for 6 to 12 months lWhat happens if antibiotics aren t taken correctly If you only kill 95 of the bacteria What s likely of the remaining 5 103114 Natural selection Frequency 54 103114 103114 ED P marv MDR TB Does this qualify as natural United States 1993 2010 9 No of Cases Percentage 500 3 400 39 300 2 r IIs there variation between individuals Yes but Without rifampin mutant is found in 200 l39107108 1 100 IIs the variation heritable 0 b k a E Cb o b k 63 6 Cb o 0 Yes it s in the DNA gets passed on when the 0 0 39 39 39 39 39 99 99 19 19 Q9 wq9 19 19 19 19 19 19 19 bacteria d1v1des No Cases Percemage We even know the exact genetic difference Updated as oijuly 2 1 2011 jquot cm 3 103114 Ell 57 E 3 Drug re51stant TB Drug res1stant TB rpoB gene with Normal rpoB gene Normal rpoB gene 0 T mutation r I A WWIRWWBW WWWWWDW WWWIMWMNBN rpoB gen rpoB gene codes for TCG part of RNA TCG part of RNA polymerase TTG mutated RN mutated RNA polymerase has a shal has a shape change Rifampin Transcription by Rifampin Transcription by Rifampin Transcription by binds RNA polymerase binds RNA polymerase binds RNA polymerase tightly slows or stops tightly slows or stops loosely is efficient 103114 103114 103114 Does this qualify as natural selection Mode of Treatment Administration in Persons Reported with TB United States 1993 2008 100 I I I I I I I I l y 80 i 1 L j I l i lt1 360 i W 5 i 15 there variation in reproductive success 5340 L a 1 In a person taking rifampin yes 20 o r r r r r w r r r lD1d natural selectlon occur 9 9 q 9 o 93 9 00 ex 0 65 oh 00 62 0 0 tes xq xgx9x 3 x bx9 x9 q9q9q909q9q9q9q9q I DOT only DOT SA USA only 103114 Com letion ofTB Thera P P Malar1a United States 1993 2008 100 o l l l l l l l l o 9 93gt 32 co 0 65 0quot 3 P q q q Updated as oi july 212011Dala avauanle mmugh 2008 only Percentage Loougtltnoauoolto 000000000 0 0 0 5 6 0 5 09 19 19 19 19 19 U Completed l Completed in 1 year or less t DMIW armament My quotmm any 1W M W unalmmuouru 103114 103114 63 Malaria Drug reSistant malaria Antimalarial First reported Introduced Difference I Plasmodium falciparum drug resistance spread by the mosquito Anopheles gambIae Quinine 1632 1910 278 I 33 billion people live in areas at risk for malaria infection I 216 million cases in 2010 I 655000 deaths 91 in Africa 103114 103114 Drug reSistant malaria Malaria distribution Antimalarial Introduced First reported Difference drug reSistance Quinine 1632 1910 278 Chloroquine 1945 1957 12 Proguanil 1948 1949 l suifad xm39 1967 1967 0 pyrimethamine Me oquine 1977 1982 5 a 3 Atovaquone 1996 1996 0 103114 103114 103114 CH 67 CH L1 L1 Malaria GeospJZa spp IHovv much genetic change does it take for 6 magmr 051715 Pfa1 1parum to become resistant to a drug lCan be a single base change 1 mutation G 01115 G fuljginosa 103114 103114 3 o Beak Size and d1et Thesmall ground nch Gempig The medium ground The large ground nch gimm ems nch G Innis cals G mugniraslris cats mainly small scum mainly medium seeds mainly large seeds I 3 EXPERIMENTAL SETUP seeds but they specialize on different sizes PREDICTION g I PREDICTION OF NULL HYPOTHESIS size 2 3 4 6 7 103114 Seed depth mm 103114 103114 71 H 72 Medium ground finches Darwin s theory of natural selection 1 There is variation between individuals IThe1r beak Slze determlnes wh1ch seeds they eat 2 Some of this variation is heritable 7 deeper beak blgger harder seeds 3 More offspring are born than can be supported lIs beak size susceptible to selection generation 4 Some individuals have a higher chance of survival I 39 39 Is the presence 0f the Other SpeCIes causmg and reproduction than others pass on these traits to seleCtion their offspring fitness CH 23 ED 24 Is there variation between Is there variation between individuals within a species individuals G foris consuming soft seeds had shallower weaker beaks than G forlis consuming hard seeds IYes there is variation in beak size and this affects the seeds they can eat IVia long term tracking in this population we know that beak size is heritable Beak depth mm lAlso Soft Medium Hard Sccd hardness 103114 103114 103114 75 76 We even know the gene now Compet1t1on and select1on Lower Bmp4 expresslon Higher Bmp4 expression dark area in embryo s beak dark area in embryo s beak lThere is heritable variation in G fortis beak size lEnvironmental variation that affects survival 33330 and reproduct10n mmmm eopiza fortis Geospiza magnirostris 78 We can see ecological history in age distributions 1983 30 N N v 39 TC Large cactus ground finch Geospiza conirostrjs N 01 Percentage of finches G I234567890l Ageyears after Grant and Grant 1989 103114 We can see ecological history in age distributions WWONWMMW In Formwuuwammnorm libwuhu whiu 7 Miundlnimiu 138 fwwnm Hwhi muof xh Em Imam I977 Molliem I74 39375 1 WT I JTK W I M I M l39 1 71 N 11 103114 103114 Copyright o l he McGrawHin Companies Inc Permission required tor reproduction or display 4 As G fortis the average hardness The average seed depleted the of the remaining seeds hardness deemed as seed supply increased new supplies were I produced in 1978 Sccd abundance gmz 6390 lDid environmental variation drought 8 cause a genetic change in the finch g g population over time 50 E E 39U x 8 g IW111 all med1um nches surv1ve and 4 3 reproduce equally well as the average seed 40 size increases 0 0 I975 I976 I977 I978 Year 103114 103114 EXPERIMENT m RESULTS 4 Average Evolut1on 1n GeospJZa fortJS 80 5 1976 Before drought N 751 all birds on 60 island 40 g 20 g lGenetlc var1atlon 1n beak s12e 0 1 11 12 13 14 E 12 lLead to var1atlon 1n d1et 4E3 1978 After drought g N 90 survivors f 8 mm in the IAS the env1ronment changes the ood I azprgaast zn supply Changes lGenotypes that match the new environment 6 7 8 9 1o 11 12 1a 14 became more common Beak depth mm CONCLUSION Natural selection occurred The characteristics of the population have changed 103114 103114 mun num muwu n 10 103114 n 83 Common misperceptions I Natural selection will optimize make things perfect Blind spot in human eyes Birth canal passes through the pelvis Testes develop in the abdomen migrate out creating weak spot in muscles Position of spinal column Plantaris muscle Pharynx same path for breathing and ingesting food Carotid artery 32112 Why can t selection make things perfect I Developmental constraints wing vs arm I Optimize What you ve got 32112 H I Evolution is not IEvolution does not mean random IEvolution does not mean changing during a lifetime 103114 H I U Types of selection a Directional selection changes the average value of a trait Normal distribution Before selection I Directional selection litness i During selection value of a traits Number of individuals Change in average After selection value Value of a tralt 103114 11 103114 CH 87 CH 88 u u Types of selection Types of selection b For example directional selection caused average b For example directional selection caused average I DlreCtlonal seleCtlon body size to increase in a cliff swallow population body size to increase in a cliff swallow population 7 20 OrigiFAil pzoagigftion 20 OrigiailEpzoagigftion value of a traits E 5 WW I Insectivo res E 15 5mm 0 Change in N 1027 0 Change in N 1027 3 1 32139 3 321de I Remember the u I Change after 6 day environment cold spell y 2 3 4 Bosdy lzeZIasss 9 m n g 2 3 4 30de lzeZIasss 9 m n g direction to go 103114 103114 H I Directional selection is Yquot htt albertsonlabs reduas mmhtm1 IPen39ssodus microlepjs in Lake Tanganyika I Scaleeating chiclids 103114 H I Directional selection htt albertsonlabs reduas mmhtml IHunt by sneaking up behind other fish taking a bite IPrey is wary 20 of attacks succeed 103114 12 103114 Directional selection a s s 39 i htt albertsonlabs reduas mmhtml IMouth is offset to either the right or left II gene for this trait 103114 Directional selection I If you are a fish living in a lake with 90 right faced fish where are you going to be looking for nibblers I To the left I What does this mean for the 10 leftfaced fish I They ll be well fed 103114 Directional selection IHypothesis Rarer faced fish will I be more successful in their attacks I get more food I have higher reproductive rates I become more common over time 103114 Directional selection ITest by following ratio of rightleft over time IHow would you expect the ratio of rightleft to change over time Fluctuates IRarer type will be more successful in breeding 103114 13 103114 i Directional selection w ell rs 4 6 4 439Aquot r h ea A u Most common type uctuates M Hori 1993 Science 103114 i Directional selection w rs 4 6 4 439Aquot r h u 6 A u Breeding adults are more commonly from the rarer type M Hori 1993 Science 103114 Types of selection a Stabilizing selection reduces the amount of variation in a trait Beiore selection I Stabilizing selection When the mean value is at the highest level of fitness selection acts against extreme values During selection Reduces variation After selection Number of individuals Normal distribution Low High fitness Low fitness fitness Reduction in variation Value of a trait 97 103114 q Stabilizing selection Eggs produced Average surviving offspring l l 2 2 3 3 4 3 5 2 6 1 103114 14 103114 I Stabilizing selection IStart with 1 3egg bird and 1 6egg bird in generation 1 11 ratio lFor generation 2 3egg bird has 3 surviving offspring 6egg bird has 1 surviving offspring 31 ratio 3egg genotype is now more common 103114 I Stabilizing selection b For example very small and very large babies are the most likely to die leaving a narrower distribution of birth weights M O i 8 n 0 Heavy mortality on extremes 01 0 Percentage of mortality Percentage of newborn population O O 3 4 5 6 8 9 1011 Birth weight pounds 1 I Jquot R v 103114 1 Types of selection a Disruptive selection increases the amount of variation in a trait Normal distribution Before selection I Disruptive selection g i Low fi ness i Most f1t values are at g 2922 at 2253 Durin selection 39 quot the extremes 9 g o t r E Bimodal distribution Increase in variation After selection Value of a trait 103114 Types of selection b For example only juvenile blackbellied seedcrackers that had very long or very short beaks survived long enough to breed 30 I Seeds are either small 20 mm or large birds with 3333 intermediate beak g 1 sizes don t do well 15 103114 Important side effect of natural Other mechanisms for selection evolutionary change lWhat causes genetic change in a species over time 1 Natural selection Overall outcome of selection 2 Nonrandom mat1ng less genetic diversity 3 Mutation 4 Gene ow 5 Genetic drift 103114 103114 Nonrandom mating sexual Female investment selection I Sexual selection A lSexes have different investments in f if reproduction Females large energetically costly gametes s Males small energetically cheap gametes Q t 39 IDifferent strategies due to different investments V Female reproduction is limited by resources Fem le Wis lay a large 93999 Male reproduction is limited by of females to thequot may sue 103114 103114 16 103114 107 1 Sexual selection I Males need to show off how great they are I Secondary sexual characteristics 39 39 Traits associated with 1 sex but not directly involved with reproduction 103114 Intrasexual selection I 2 members of the same sex compete for mates I Secondary sexual characteristics involve adaptations to help with competition 103114 Intersexual selection I Males are showing off for females I In guppies this is coloration spots on tail I Variation between males in coloration I Why Why isn t every male super colorful 103114 Other mechanisms for 123 evolutionary change IWhat causes genetic change in a species over time 1 Natural selection 2 Nonrandom mating 3 Mutation 4 Gene ow 5 Genetic drift 103114 17 103114 3 3 Mutation Mutation normal fly Y m gyfgmd IChanges genotype frequencies by creating new genotypes Mutation is the only source of new genetic variation ISubstitutions I Parent AATCCGGATCAT antenna leg m place of antenna IOffspring AATCGGGATCAT 3 3 Mutation Mutation IMutation rate is small but our genome is large 1 2 x 10398 base generation We have 3 billion bases IWe all have 60 mutations 32112 I Does this matter IProbably not most mutations are neutral no selective advantage or disadvantage I noncoding regions I synonymous mutations don t change the protein I changes in proteins away from the active site may not have an effect 32112 18 103114 39 Mutation 39 Mutation and selection EXPERIMENT I Mutations affect l individual selection gm makes them more 39 common IMutatlon IS rare and mutatlons that actually n hin r r r r I Elena SF VS Cooper do a Vt g a e a e and RE Lenski 1996 lHave to take the long view Punctuated evolutlon caused by selection of rare beneficial mutations Science DICVIDN Descendanl mpmm have mngava was time 272 1802 1804 32112 103114 Mut 8121011 Mutations found by sequencing genomes sampled between 2000 and 20000 generations from an evolution experiment with E coli EXPERIMENT RESULTS a O 13 o 0 o o 4 12 o o u 0 mm 5 C O Rolahn39 Munw 1J1 livxcvmldnt a 11 Irmpuhhnn innummd wxlh g angina pnpulalmn HICN39J N39U in suddnn bursis nvtv limo 3 10 Q 39 v r a 0 500 1000 1500 2000 amt r m WWW CONCLUSION Descendant populations have higher tness I I than do ancestral populations JE Barrick et al Nature 000 15 2009 don101038nature08480 01ml lem39 Ed srm Iquot nature 103114 103114 19 103114 132 I Some people are naturally resistant to HIV 133 HIV infection Gene CCRS I The resistance I Membrane protein mutation is common in that HIV uses to Europe rare in Africa enter cells and Asia I Mutation in CCRS I Why no entrance for the 39 virus I CCRSA32 CH C 135 CCRSA3Z CCRSA3Z I Yersinia pestis bubonic plague I Killed 30 60 of Europe s population in mid1300s w Reduced world population from 450 million to 350375 million I Plague still exists but fairly rare 103114 I Presence of CCRSA32 provides resistance to Y pestis I Why is it more common in Europe 103114 20 103114 q CCRSA3Z I Or maybe Vaccinia virus Smallpox I Widespread in Europe from 16th 19th centuries I During 18th century killed 400000 year 10 of infants in Sweden 103114 137 q CCRSA3Z IEither way this allele is around because in the past it provided a benefit IProtection from HIV is a sidebenefit which might be selected for now 103114 138 q Bedbugs Cimex lectularius 103114 139 q Bedbugs I Feed on blood from warmblooded hosts I Each life stage needs a blood meal to advance I Females can lay 5 eggs day u Mattress seams crevasses in box springs etc H Eggs hatch in 4 12 days 103114 21 103114 Bedbugs I 11000 homes in NYC filed complaints 2010 I 31 of households in Downtown Eastside neighborhood in Vancouver I Resurgence over past 10 years in North America and western Europe J 103114 Bedbugs I Health hazard is generally reaction to the saliva I Generally don t carry disease I But MRSA has been found in Vancouver bedbugs J 103114 Bedbugs I Insecticides I Pyrethruns and pyrethroids Derived from chrysanthemums I Block sodium channels in nerve cells muf n 103114 resistance 143 How many mutations to get pesticide 103114 22 103114 Distribution of mutations Minimum of mm mutation In bed bug population 103114 Z Other mechanisms for evolutionary change lWhat causes genetic change in a species over time 1 Natural selection 2 Nonrandom mating 3 Mutation 4 Gene ow 5 Genetic drift 103114 Gene ow lGene ow migration IIf immigrants have different proportions of genotypes they will change the gene pool of the population they move into 103114 Gene ow line I o O o 00 0 00 390 o o 39 o 00 9 o 0 0 00 o39 o 00 0900 000 o999 Population 1 Population 2 147 At time 1 populations differ in allele frequencies 103114 23 103114 Gene ow Gene ow Time 1 39 quotquot39quotquotquotquotquot quotquot quotquot quot quotZ o 0 o o 0 90 o o O 9 O o g Attinllef1 gt 0 U8 IOnS o C o O 9 9 0 Emir in allele 0 0 O 0 o 09 frequencies I Overall effect 0 O O O 0 Population 1 Time 2 Population 2 0 GeneO o 0 o 0 flow Population 1 Population 2 Gene flow causes allele frequencies in the two populations to be more alike 103114 populations become genetically similar I Does this matter Parus major 103114 Gene ow Gene ow I Females born in the a Gene flow from malnland to VIIE eastern population lay fewer eggs I Why Vlleland I But female survival is higher in eastern population I Birds in eastern population are better adapted for island life 103114 I Hypothesis Fewer migrants bringing in maladaptive mainland genotypes Eastern population lt Western population 4 Ge e flow Maipland Netherlands 103114 24 103114 Gene ow Gene ow 055 a Gene flow from mainland to Vlie 050 Vlieland 4 m 045 39 I Prediction Survival 1 212quot 5 0 4o i will be linked with the H P E 39 number of immigrant g 03935 grandparents G3quot quot quot 030 quot l Hauling Netherlands 025 k 020 I l l39 T I o 1 2 a 4 of island born grandparents 103114 103114 Other mechanisms for Genetic drift evolutionary change lWhat causes genetic change in a species over time 1 Natural selection 2 Nonrandom mating 3 Mutation 4 Gene ow 5 Genetic drift 103114 IThe genotype you get is determined randomly Random draw during reproduction IRandom draws create deviations from expected values 103114 25 103114 1 15 Genetic drift Genetic drift I 2 boys Probability of a boy probability of a boy 05 05 025 I Sex chromosomes XampY I 2 girls I 50 50 Chance of b CV or girl Probability of a girl probability of a girl 05 05 025 IWhat s the probability of having 2 boys 2 I 1 of each girls or 1 boy and 1 girl Probability of a boy probability of a girl probability of a girl probability of a boy 05 05 05 05 025 025 05 103114 103114 Genetic drift Genetic drift I Most likely to have 1 of each but 2 boys or 2 gl s 1511 t uncommon INot biological statistical I How about 3 girls 5 girls 10 girls 05 05 05 0125 125 05 05 05 05 05 003125 3125 05 9r 05 9r 05 9r 05 9r 05 9r 05 9r 05 9r 05 9r 05 9r 05 lGenotypes Of OffSleIlg39 are the result Of a I Probability of having all kids be the same sex L h 11 gets smaller as the number of kids sample 39 arge uCtuatlons Wlt sma group 3 size gets bigger 103114 103114 26 103114 41 41 Genetic drift Genetic drift b Genetic drift reduced allelic diversity in most populations 0 g 100 I As populations get 0 o At start of experiment almost all g 1 populations have both alleles smaller genet1c dr1ft B l h M k t w 5 so Both 0 leads to loss of a rlstes ape 52 use rigenetlc mar er In rult les g aueles 9 g o I genetic diversity E 333 g 60 present 0 1 39quot93922m o 40 o o forked lost I 96 populations of 8 8 m g 1 o 3 3 z o 3 Only forked individuals each quot5quot 3 20 o 0 z 0 allele present I O O o r t o 0 normal lost s o 1 I I l I I 16 generations g 0 4 8 12 16 Inquot N Generatlon 103114 103114 41 41 Genetic dr1ft Genetic dr1ft IAs populations get smaller genetic drift becomes more important I Consequences Since alleles are lost 39 Honda panther randomly not only is genetic diversity being lost but good alleles might be lost 103114 103114 27 103114 Florida panthers ISubspecies of mountain lion endangered since 1967 lPopulation decline due to habitat loss hunting IVery isolated 2000 km from any other mountain lions ISmall population for 1525 generations 3050 individuals in the mid90s 103114 Genetic drift I Deformity at the end of tail I Also reduced sperm viability sterility undescended testicles increased heart defects growth rates I How can a lack of genetic diversity be xed 103114 Genetic rescue I8 female Texas cougars in 1995 IIncreases in genetic diversity IFrequency of undescended testicles 49 to 0 lFrequency of kinked tail 77 to 7 103114 Genetic drift 167 103114 28 103114 Review of evolutionary processes evolutionary process effect reduces genetic diversity due to natural selection interactions with the environment can be predictable causes populations to resemble each n ge e 0W other genetically mutation introduces new genetic variation genetic drift reduces genetic diversity randomly seen in small populations 103114 29


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