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Lecture 1 1 Mendel Assumed o Traits are largely due to the action of a single factor gene 0 But most traits are polygenic Height Skin color Disease predisposition Heart disease High blood pressure Diabetes Cancer Concept of Polygene Inheritance o Most traits are determined by several genes at different places on the chromosomes eg human height can see variation not just tall or short Mendel Assumed o Traits are determined by only two possible alleles eg tall vs short 0 But many traits have more than two possibilities Concept of Multiple Alleles 0 Many traits have multiple alleles not just two eg ABO blood type there are 3 alleles A B 0 So these are the possible 6 genotypes AA AB AO BB BO 00 AA amp A0 are blood type A A is dominant over 0 AB is blood type AB BB amp B0 are blood type B o 00 is blood type O Mendel assumed that his factors only affected one trait o But we now know that some genes affect many traits o Concept of pleiotropy eg Marfan s syndrome Abraham Lincoln several symptoms OOO And Mendel never knew where his factors were located We do now 0 Chromosomes discovered in 1875 We know his factors now called genes are arranged in a linear array along the chromosomes 0 This concept of the chromosome theory of inheritance was proposed in 1903 We now know where all the major genes are located on the human chromosome Human X chromosome has 1098 genes 0 The banding is due to staining and can be seen with a microscope 0 How do you see chromosomes o You have to use stains to see them 0 Chromosomes are seen only in condensed form when preparing for nuclear division o Otherwise the genetic material is unraveled and called chromatin Chromosome Numbers Vary Among Species 0 Ant 2 o Mosquito 6 o Orange 18 27 36 o Frog 26 o Coffee 44 0 Humans 46 o Spanish Butterl y 380 o Adders Tongue plant 1020 Chromosomes come in pairs o Human karyotypeChromosome pattern 0 Humans have 46 chromosomes 23 pairs Humans have 46 chromosomes in most cells 23 pairs 0 Diploid number46 2n o Haploid Number23 n 0 Polyploid Numbers3n 4n Snetc can occur in some intestinal and liver cells o One set of 23 from father one set of 23 from mother o 22 pairs are autosomes o 1 pair are sex chromosomes xx female xy male can tell in a karyotype because xy has a difference in size Mendel s Factors genes occur in a particular place locus Sister chromosomes carry their alleles in the same position Many genes exist on each chromosome o VirusesS910 genes 0 Bacteria100096000 genes 0 Human21000 genes Concept of sexlinked traitstraits carried on the sex chromosomes eg Duchenne muscular dystrophy pattern baldness color blindness hemophilia A all on x chromosome Concept of sexlinked traits traits carried on the sex chromosomes 0 Males have only one x chromosome so if they have the allele for the trait they will show it 0 Females have 2 x s and so if one is defective the other can compensate Concept of Linkage o Genes on the same chromosome are linked eg 2 sister chromosomes Cell division in the body cells 0 Mitosis before this happens the chromosomes must duplicate daughter cells have the same number of chromosomes as parent cells O O 0 Step 1 the chromosomes duplicate producing two identical arms on each one each with the same alleles each arm is called a chromatid Step 2 Chromosomes line up Step 3 Chromatids are pulled apart 46 chromosomes in each cell 0 Cell division in the sex organs 0 O 46923 and 239 each 23923 and 23 4 sperm each with 23 chromosomes Meiosis reduction division daughter cells with 12 the number of chromosomes as parent cells 2 rounds of cell division meiosis 1 cells become haploid meiosis 11 The chromatids are split apart Steps Chromosomes are duplicated meiosis 1 Sister chromosomes line up side by side Sister chromosomes separate going to different daughter cells meiosis II Chromosomes line up again Chromatids are pulled apart 23 chromosomes are in each cell Meiosis in Ovary Diploid9Haploid 46923 and 23 Egg plus 3 polar bodies 0 Distribution of Chromosomes in gametes O O The gametes end up with only one set of chromosomes It is random which chromosome of a pair goes into which gamete Each gamete has a mixture of the mother and father s chromosomes 2238 million combinations Sexual recombinationvariety Concept of Crossover sister chromosomes swap pieces during meiosis O O O This occurs when the sister chromosomes line up during Meiosis I Crossover breaks up linkages on the same chromosome So assume RY are linked and ry are linked Indpendent assortment wasn t possible The only gametes that could be formed are RY and ry Crossover can break these linkages producing new gamete possibilities RY ry Ry and rY 0 How is sex characterized in Humans O In addition to anatomy physiology and chromosomes there is another answer Genes specific genes determine whether an embryo will develop as a male or female 0 SRY SexDetermining Region of the Y chromosome Gene 0 Early in development the immature gonads of males and females are indistinguishable 0 Males in the 7 week of development the SRY gene on the Y chromosome activates a number of genes and the gonads develop as testes 0 Females With no SRY gene gonads develop as ovaries by default 0 Can an XY karyotype occur with female anatomy Crossing over can occur anywhere along the autosomes The sex chromosomes normally cross over only at their tips Sometimes the SRY gene is involved What sex is XX SRY What sex is XY SRY Sex reversal occurs in 1 in 20000 births Lecture 12 What is a gene 0 1866 Mendel Traits are determined by particles factors that are passed from one generation to the next o 1909 Danish Botanist Wilhelm Johanssen Coins word gene for the unit associated with an inherited trait o 1910 Thomas Morgan work on fruit ies shows that genes sit on chromosomes 0 1941 George Beadle amp Edward Tatum introduce idea that One gene makes on enzyme o 1944 Avery MacLeod amp McCarty find Genes are made of DNA o 1953 Watson amp Crick publish structure of DNA What is the chemical nature of DNA o Genes are composed of nucleic acids DNA Double helix model Watson amp Crick 1953 Base units GuanineG CytosineC AdenineA ThymineT Two strands of DNA connected together by hydrogen bonds between the base units Two basic questions about DNA How does it make copies of itself before cell division How does it control the cell DNA Replication 0 When cells divide they must make a copy of the DNA sequence o Suppose the double helix reads this way GGCTCAAATGTTAAAAGGTCATGGACCGTAT CCGAGTTTACAATTTTCCAGTACCTGGCATA First the strands unzip Then each separate strand makes a copy of itself We end up with two duplicate double strands How does DNA control the cell O O O DNA9mRNA9Protein DNA transcription mRNA translation Protein Transcription in the nucleus translation in the cytoplasm s ribosomes Instructions from the DNA Ribosome tRNA Amino acids as Links amino acids raw material together to make protein The code O A set of nucleotide bases determines which amino acid will be used to put into the protein How many will be needed Triplets amp Codons O O How many bases are need to code for 20 amino acids There are only 4 to use How about 2 42 only 16 Not enough How about 3 bases 4364 DNA triplets More than enough But we only need 20 different DNA triplets Or 20 RNA codons Several codons code for the same amino acid Ex phenylalanine is coded by UUU UUC Ex leucine is coded by UUA UUG CUU CUC CUA CUG The same messenger RNA codons are used in Virtually all organisms So what is a gene O A gene is a sequence of nucleotide bases that code for a polypeptide lAAATAAAampGTClGACE AT The order of the nucleotide bases determines which amino acid is put into the polypeptide Central Dogma of Molecular Biology o DNA9Transcription9RNA9Translation9Protein 0 Deduction The more closely species are related phylogenetically the more sin1ilar their DNA RNA and proteins will be o Test Examine DNA RNA or proteins among species 0 Protein AnalysisAmino acid sequencing Ex Cytochrome C enzyme 104 amino acids 0 Human vs rhesus monkey 1 difference Human vs dog 11 differences 0 Human vs rattlesnallte 14 differences 0 Human vs bullfrog 18 differences Human vs tuna fish 21 differences 0 Human vs fruit y 29 differences 0 Human vs pumplltin 36 differences 0 Human vs bacteria S6 differences o Nucleic Acid Sequencing DNA amp RNA Can compare protein coding regions or non coding Can analyze nuclear or nonnuclear mitochondria chloroplasts or plastids Complete genome sequences now known for some viruses some bacteria a nematode worm rat chimpanzee and humans Summary All organisms use DNA as their genetic material The codons for an1ino acids are common for all organisms 33 of the genes in plants and humans are similar 67 of the genes in fruit ies and humans are similar 90 of the genes in mice and humans are similar 98 of the genes in chimpanzees and humans are similar Data supports the hypothesis of evolution OOOOOOO Lecture 13 Mutations abrupt changes in the genetic material occurring typically during cell division o Each baby has about 130 new mutations Most are neutral o Somatic Mutations why are these irrelevant to evolution Types of Mutations o Structural changes in chromosomes Loss or duplication of whole genes deletionsduplications Ex Matthew State of University of California San Francisco has discovered variations in chromosome 7 An extra copy of a particular segment 25 genes greatly increases the risk of autism which leads to social isolation But if this section is lost it results in Williams syndrome which leads to intense sociability Changes in gene arrangement Translocation large pieces of chromosome moved to another place in the genome Transposons jumping genes small pieces of DNA shifting within the genome Inversions chunllts of chromosome ipping over o Numerical changes in chromosomes Aneuploidy addition of one or more chromosomes Ex Extra sex chromosomes xxy xxyy xxxy etc Down syndrome extra chromosome 21 o But it s not all due to Mom Sperm parent cells divide every 15 days This continuous division and copying of DNA leads to errors and the rate of error increases significantly with age A 20 year old man will have an average of 25 new point mutations in his sperm A 40 year old man will have 65 A 40 year old woman will have 1 5 Polyploidy multiple copies of the entire genome Characteristic of many plant species 0 Ex Banana can be 2n22 4n44 SnSS 0 Gene point mutationsNucleotide changes Substitutions a substitution in the mRNA can lead to a different amino acid Additions leads to a frame shift 9 Subtractions deletions leads to a frame shift 6 0 Protein chain length modifiers start and stop codons leads to short or extra long nonfunctional proteins Ex premature stop in the protein sequence produces a short nonfunctional protein Ex runon protein this substitution produces a longer protein since the CTT now codes for a glutan1ic acid residue instead of stopping transcription Mutations in Developmental Genes 0 Heterochronic mutations alter the rates of growth of some organs relative to others in the organism Many of the differenes between species seem to be due to regulatory genes Ex Neoteny sex organs development faster than the somatic cells producing a sexually precocious organism Axolotyl Possible role in evolution Larva Metamorphosy Neoteny No metamorphosis Normal Adult New Species Heterochrony alter the timing between different cell lines Allometry comparing growth rates between tissue or structures Shifts in growth gradients o Transformation of species by genetic changes regulating embryonic chemical gradients o Transformation of Cartesian coordinates Homeotic Mutation o Homeotic genes regulate clusters of genes controlling development Drosophila sp Have at least 8 homeotic genes Ex mutation in antennapedia gene leads to formation of leg not antennae Ex mutation in bithorax gene leads to two thoraxes and additional wings o HomeoboX18O nucleotides Identical in all homeotic genes and produce identical 60 amino acid sequences in the signaling proteins This equence binds to specific sites on DNA Similar sequences are found in all multicellular organisms Possible evolutionary importance 9 Hopeful monsters Causes of Mutations OOOOO Ionizing radiation Chemical mutagens Spontaneous mutations during DNA replication Note some mutations can be repaired Mutation rates Achondroplastic Dwarfism 40 12O ratesmillion Total color blindness 3O ratesmillion Hemophilia B 20 40 ratesmillion Hemophilia A 5 1O ratesmillion Most genes 1 ratemillion 1 gamete in 10 carries a new mutant Effects of Mutations o Harmful minor major lethal Most mutations recessive not expressed except as aa o No effect Neutral mutation Silent mutation mutation for equivalent codeon or equivalent group of amino acids Mutated gene expressed but the same fitness within the environment blue or brown eyes o Beneficial increases the fitness of an organism Mutations and Evolution o Mutations determine survival and reproduction Fitness Positive fitness Negative fitness Neutral fitness no change in fitness 0 Most mutations have negatve fitness 0 Mutations are random ie not directed by environment Today s classical view o Sexual and genetic recombination cross over provide variability by reshuf ing existing alleles o Natural selection acts on the alleles present in the population causing shifts in their frequency of occurrence 0 Acquired characteristics cannot be passed on via DNA to the next generation ie The environment can t change the DNA in specified directions o Mutation provides the variability new alleles This doesn t happen inheritance of acquired characteristics Use amp Disuse Environment Need Heredity New Species This does happen natural selection MUTATION CROSSOVER HERE TY SEX Genetic recombination Fertilization i NATURAL SELECTION jgt VARIATION jgt NEWSPECIES To measure the rate of evolution we need a clock Molecular Clocks o If mutation is fairly constant the number of nucleotide differences between species indicates the time that the species have been separated o Suppose I want to estimate the length of time that 2 species have been separated in time A Compare pieces of DNA coding for a functional enzyme that is present in both species eg cytochrome oxidase B Compare pieces of DNA coding for a structural protein that is present in both species eg hemoglobin BUT it is best to compare non coding regions of DNA It is best to study many nucleotide sites and take an average rate 0 Conclusion data strongly support the hypothesis of evolution All organisms share a common ancestor Lecture 14 Mutation and Measuring the Rate of Evolution o We need a clock Molecular clocks o If mutation rate is fairly constant the number of nucleotide and protein differences between species should indicate the time that the species have been separated Protein Analysis 0 Amino Acid sequencing Eg Cytochrome C enzyme 104 amino acids Human vs chimpanzee 0 difference Human vs rhesus monkey 1 Human vs dog 1 1 Human vs rattlesnake 14 Human vs bullfro g 1 8 Human vs tuna fish 2 1 Human vs fruit y 29 0 Human vs pumpkin 36 Human vs bacteria 56 differences To estimate the length of time that 2 species have been separated in time o We can compare pieces of DNA coding for a function enzyme that is present in both species eg cytochrome oxidase o We can compare pieces of DNA coding for a structure protein that is present in both species eg hemoglobin o It is best to compare non coding regions of DNA o It is best to study many nucleotide sites and take average rate But you need to know the average rate of mutation Conclusion 0 Data strongly supports the hypothesis of evolution o All organisms share a common ancestor Out story continues you will remember 0 At the time of Darwin s death in 1882 at the age of 73 most biologists were convinced that evolution had occurred but the mechanism of evolution was uncertain So how does evolution work Lamarck s view o The French biologist Lamarck argued that characteristics acquired during the life time of an organism could be passed on to its offspring Evolution by acquired characteristics Use and disuse o Inheritance of Acquired Characteristics Environment use and disuse and need lead to heredity which leads to new species Darwin s view expressed in modern terms o Crossover genetic recombination mutation sexfertilization lead to heredity which leads to variation which leads to new species Natural selection also leads to variation and new species How did the giraffe get its long neck 0 The classical answer all of these are consistent with Lamarck s view of evolution o The trait of long necks in the common ancestor of giraffes first appeared Because they needed long necks to eat the leaves of trees Because they needed long necks to fight Because they needed them to maintain their balance as they ran with long strides How could the need for long necks actually cause long necks to appear Darwin s argument was that a giraffe s ancestors had variable neck lengths and the ones with the longest neck had a selective advantage They were the ones that were most likely to leave offspring behind So the average giraffe neck progressively grew longer over time because the ones with the longest necks in a given generation were always at an advantage Both Lamarck and Darwin had a problem how could they explain why a trait appears 0 Lamarck said need and use and disuse does it But how do these factors prompt the development of the trait to be passed on Darwin said that chance variations come along But how does that happen and why Consider the giraffe problem without considering the mechanism of how it occurs the classical argument is that the giraffe s neck elongates over generations because of food competition But is this assumption correct 0 Deduction if the food competition hypothesis is correct then giraffes should be competing for food with other species 0 O O O ie When food is scarce giraffes with long necks can reach food higher on the trees unavailable to shorter necked animals And so they survive better Test look at where giraffe s eat Data giraffes usually do not extend their necks to feed Evaluation data do not prove they hypothesis or even support it very well BUT it hasn t been tested in harsh conditions where food is scarce Sexual selection hypothesis 0 0 Observation males fight among themselves over breeding rights for females They use their necks to fight striking blows to others with their heads So longer necked giraffes should be able to strike harder blows Maybe that s why giraffes have longer necks Test see if longer necked giraffes win the most fights Data they do Data support the hypothesis but maybe there are other possibilities But no matter which hypothesis is correct this still doesn t resolve the question of what the mechanism of evolution exactly is Is it use and disuse leading to acquired characteristics Or is it variation followed by natural selection Or Weismann s experiments 0 0 August Weisman was a famous German scientist in the early 1990 s He believed passionately that natural selection was the only driving force of evolution Weismann argued that the inheritance of acquired characteristic could not occur on theoretical grounds saying that the germ cells sperm and eggs were totally isolated from the body cells soma So any environmental in uence acting on the body could not affect the heredity Today we argue something similar when we say that any mutation in a body cell does not affect the genes of the sex cells o Weismann s ideas were published in 1912 in a book entitled The Germ Plasm A Theory of Heredity o He argued that the germ plasm is continuous from generation to generation and that bodies are merely vehicles for transmittin ghte germ plasm from place to place o Samuel Butler said something similar when he said A hen is only an egg s way of making another egg o Or as EO Wilson has put it People are DNA s way of making more DNA 0 Weismann decided to test Lamarck s ideas by cutting off the tails of mice He knew that two short tailed cats had been exhibited at a recent scientific meeting with the claim they were the progeny of cats with amputated tails Weismann decided to amputate the tails of 20 generations of mice always breeding together the shorttailed animals with each other carefully measuring their tails all along Weismann did find out that there was no shortening The data do not support Lamarck s hypothesis o It s not that cut and dried 0 Darwin also accepted that acquired characteristics was also part of evolution But natural selection was most important o There were some things that he could not explain such as how variation was caused remember he knew nothing about genetics o So he believed that the environment could stimulate variation one of Lamarck s ideas and this would be inheritable Paul Kammerer s Experiments 0 Paul Kammerer was a well known scientist in Vienna in the early 1900 s o He believed in the inheritance of acquired characteristics o Frog s and toads generally breed in water The males grab a female that is about to lay eggs from behind He mounts her and clings to her back until she releases her eggs Then he discharges his sperm on them as they emerge from her cloaca To help him hold onto the wet slippery female he has roughened places on his forelegs called callosities o The midwife toad is an exception it breeds on land and the males lack the callosities 0 Critics attack But Kammerer was supported by many well known scientists He defended his work People had difficulty repeating his work because of the difficulty in working with the toads The USSR praised his work and Paul Kammerer was invited to the USSR to take over the chairmanship at the University of Moscow While he was away a committee of scholars visited his laboratory and examined on e of the toads that remained from his experiment They concluded that black india ink had been applied to the toad s legs to enhance the visibility and the callosities appeared artificial When Kammerer heard this he was offended and deeply hurt Kammerer returned to pack his belongings to go to the USSR and he heard about the comn1ittee s conclusion He promptly walked into the woods and put a bullet through his brain Epigenetics changes in the expression of a gene that occur without changing the DNA sequence o Eg adding methyl groups CH3 to cytosine can be inherited and this can cause gene inactivation o Eg histone modification of chromatin It appears that the environment can induce heritable epigenetic changes inheritance of acquired characteristics Lysenko s Wheat 0 Trofim Lysenko was a Russian agricultural specialist with strong political leanings toward the ruling Bolshevik party run by President Stalin and based on the philosophical basis of Marx Engels and Lenin 0 They came to power in the 191 7 Russian revolution determined to improve the lot of the peasant farmers Converting wheat to feed the people o Lysenko was able to convince Stalin that the Lamarckian principles could be applied to Soviet agriculture 0 He believed that elements of both Darwinism and Lamarckism were correct Many of his experiments were directed toward converting winter to spring wheat causing seeds to gern1inant earlier Lysenko s Experiments o Lysenko s experiments were based upon an old peasant farmer practice known as vernalization applying cold temperatures to seeds o The seeds were treated with cool spring temperatures and the ones that germinated and developed their seeds were collected and treated again This was repeated over several years Progressively he developed good varieties of wheat that possessed a frost resistance and could be grown earlier than normal Conclusion o Lysenko argued that there are two methods for the vernalization of wheat First is to moisten and chill the winter seeds at 010 degrees Celsius for 3050 days and this stimulates early growth in the spring but does not change the heredity o Lysenko said The second method is to change the nature of the winter plants whereupon they will cease to be winter plants in respect ot their heredity He used this method 0 Winter seeds were given not 0 degrees Celsius but only cool spring temperatures 0 The seeds that germinated were used for the next generation this was repeated over and over to get the desired effect changing winter wheat into spring varieties These trials he believed had disrupted their heredity Today s View 0 Today we think Lysenko was doing a simple artificial selection experiment choosing the seeds that germinated early and using them for the next generation throwing the other seeds out But maybe epigenisis was involved The Tragedy 0 The tragedy of Lysenko s rise to power was that he sti ed any opposition to his interpretation of genetics He argued that anyone working on theoretical genetics eg Drosophila was not doing the practical work needed by the Soviet economy o He argued that only Lamarckian principles were compatible with the stated goals of the revolution o Lysenko s view was that Darwinism left evolution to chance Lamarckism meant that we are not bound to out genetic destinies but can change things for the better 0 The End of Soviet Genetics o Prior to the Lysenko period the Soviets were the leaders in the field of genetics During the period from 19251965 Lysenko s opponents were systematically jailed removed from power or just disappeared All opposition was silenced and the field of basic genetics largely disappeared SCIENCE AND POLITICS DO NOT MIX o Or do they o Climate change research What is evolution o Change through time o Decent with modification 0 Change in the genetic makeup of biological populations through time How does evolution occur o This DOES happen natural selection Mutation crossover genetic recombination and sex fertilization lead to heredity which along with natural selection leads to variation causing new species to arise o This DOESN T happen inheritance of acquired characteristics Environment need and use and disuse lead to heredity which lead to new species 0 This DOESN T happen or does it Environment use and disuse and need epigenetics lead to heredity which lead to new species Random genetic effects Population genetics the study of the change in the allele frequency in a population through time o Gene pool total collection of the alleles of a gene in the population o Rabbit island 1000 rabbits600 brown and 400 white 2 alleles and complete dominance Brown B dominant White b recessive 3 genotypes BB ampBbBrown bbwhite Suppose S00 homozygous brown rabbits BB 1000 B alleles 0 100 heterozygous brown rabbits Bb 100 B alleles 100 b alleles 400 homozygous white rabbits bb 800 b alleles O Total 1100 B alleles 900 b alleles or 55 B 45 b Suppose the allele frequency in the original colonists was Pfraction of gene pool with dominant allele p55 Qfraction of gene pool with recessive allele q45 Total pq1 055045100 Genotypes in the next generation The frequency of drawing the BB genotype in the next generation is 03025 p2055203025 or about 30 What is the frequency of the white genotype Q2045202025 or about 20 What is the frequency of the Bb genotype 2pq205504504950 or about 50 Hardy Weinberg Principle 0 P22pqq210 this describes the situation when there is NO evolution Allele frequency and genotype frequency will remain constant fro generation to generation if No natural selection No differential migration no gene flow No differential mutation Random mating Large population no genetic drift of random genetic changes 0 Using the Hardy Weinberg equation 0 0 Rolling your tongue is due to a dominant allele R nonrollers are rr So 36 of the class can roll their tongues RR or Rr and 64 can not roll their tongues rr Let us assume that there is no selective advantage to tongue rolling so that the Hardy Weinberg conditions hold Now remembering that the gene pool is composed of only R s and r s can you calculation what percent of the gene pool is r and what percent is R And if there are 400 students in this room how many are Rr 032 X 400128 Answer if 36 of the class can roll their tongues RR or Rr and 64 can not roll their tongues rr remember p22pqq2 RRRrrRrr 43 264100 If change in allele frequency does occur ie there is evolution then the rules of the Hardy Weinberg principle have been violated Consider the problem of population size 0 Random changes will be important in small populations lt500 individuals 0 Small populations do not have a large number of possible variations in their alleles Founder effect during the founding of new colonies Bottleneck effect because of population crashes Genetic drift in small populations Founder effect the loss of genetic variation that occurs when a new population is established by a small number of individuals from a larger population 0 This new population is only a sample of the original population diversity and may be drastically different o Eg genetic diversity of Icelanders and Easter Island natives is much less than the population at large o Eg Amish population established by only a few colonists and the prevalence of polydactyly is much higher than the original population Bottleneck effect the loss of genetic variation that occurs when a great decrease in the population size occurs o The new population is only a sample of the original population diversity and may be drastically different o Eg the frequency of total color blindness among the inhabitants of Pingelap an island is Micronesia Around 1775 a typhoon reduced the population of the island to only 20 Among survivors one of them was heterozygous for color blindness After a few generations the prevalence of color blindness was 5 of population and 30 as carriers in the USA only 0003 of the population has complete color blindness Genetic drift the change in the frequency of a gene variant allele in a population due to random sampling But the HardyWeinberg Rule is seldom in effect 0 The most tenacious misconception in biology may be the idea that all processes serve a purpose This idea is so deep seated that students fail to even consider random processes as responsible for biological patterns 0 Genetic drift is a random process and is responsible for many characteristics of populations It happens in all populations not just small ones although the smaller the population the faster and more profound the effect is likely to be 0 This is how this is done P22pqq2 Q2rrSS00001 Q01 Since pq1 and we know q01 we know p09 Since 2pq is the Rr frequency this means 20901018 frequency of Rr 018 X 500 90 Rr Review o Selection and genetic drift working on variation in the population cause evolution Selection 0 Artificial Selection genetic changes within a population which occur because human beings intentionally select for certain characteristics either by choosing which organisms to breed or eliminating undesirable individuals Selection for increased speed in racehorses is no longer effective Kentucky Derby winning speeds have not improved significantly since 1950 o Natural Selection genetic changes within a natural wild population that occur because of differences in the reproductive success of some individuals over other individuals In order for evolution to occur there must be variation in the population How effective is Selection Consider artificial selection o All of these plants come from wild mustard cabbage brussel sprouts kohlrabi kale broccoli and cauli ower 0 Farm animals eg chicken egg production 1933 126 eggshenyear Today 36Seggshenyear o Artificial selection in dogs All dog fossils from 10000 years ago are from one species of Asian wolf The Romans 2000 years ago had only six breeds In 1837 the book British Quadrupeds listed lt 20 breeds Most breeds have been developed in the last 1 50 years Evolution can be fast over 100 breeds of dog 0 Domestication of silver foxes Natural Selection o Differences in mortality and reproduction lead to differences in the proportion of alleles passing to the next generation o Positive selection a selective advantage for one allele and that favored allele increases in the population o Negative selection a selective disadvantage for an allele and that tends to disappear from the population Natural selection in bacteria o Development of antibiotic resistance in bacteria o Many antibiotics are no longer effective against certain strains of bacteria Natural selection in insects resistance to pesticides 0 foliate insecticide Natural selection of plants to herbicides Natural selection in plants for copper tolerance look at video What produces selection o Internal Environment Eg genetic environment Eg physiological developmental environment o External Environment Physical environment water temperature oxygen Biological environment Competition Predation Parasitism Food supply Mate selection sexual selection o Success must be judged in 2 ways Absolute Terms Will the genome work Relative Terms Is the genome the best available model Slight advantage over long timeenormous changes elephant trunk 100 inches Selection in 2 allele traits o Selection against a dominant trait o Genotypes AA Aa aa 0 Rapid elimination of the trait should occur o Speed depends on how deleterious the allele is Fitness and Natural Selection 0 How to calculate relative fitness compare the success of the favored allele to that of the unfavored allele number of children produced by 100 unfavored genoytpe number of children produced by 100 favored genotype o Suppose that W 20 100 020 fitness coefficient 0 Eg Achondroplastic Dwarfism due to a dominant allele DD and Dd dwarf condition ddnormal Number of children per 100 dwarf parents 20Number of children per normal parents 100 W 20 100 020 fitness coefficient o Remember that the fitness of the best allele is always 10 0 Since the individuals with the favored allele produce more offspring than the un avored individuals they have a W 10 O The un avored allele would rapidly be eliminated from te population unless there was a high mutation rate Selection in two allele systems continued 0 O O 0 Selection against the recessive Genotypes AA Aa aa Selection will be slow to remove the a allele in complete dominance because it is hidden in the heterozygous condition Aa These are carriers Cystic Fibrosis Cause by recessive trait cc Normal allele C causes channels in the cell membranes lung gut to allow Cl out of cells and water follows If both alleles are cc then this doesn t happen and thick sticky mucus clogs lungs and gut and these tissues are breeding grounds for bacteria Most common genetic disorder in Caucasians affects 1 out of 2500 white babies 5 of Caucasians are carriers CC is normal Cc is normal but carrier cc is cystic fibrosis Cc X Cc 25 of kids are cc and have cystic fibrosis Why aren t they eliminated from the population Because Cc have protection against diarrhea Selection favoring heterozygotes Aa Can only occur if incomplete or codominance because the trait is expressed Eg sicklecell anemia Sicklecell codominance NormalHbNHbN Mild Anemia HbNHb5 Severe Anemia Hb5Hb5 In the USA W 10 W 09 W 014 In Africa W 088 W10 W014 Heterozygotes are favored in Africa because they are more resistant to malaria The environment determines what is fit Natural Selection in Polygene Traits O O O O Directional Selection Stabilizing Selection Disruptive Selection This is negative selection elimination of unfit genotypes Selection in Human Embryos 100 eggs in contact with sperm Lecture 17 84 successful fertilization 69 successful implantation 42 successful development 4 h week 3 5 successful development 8 h week 31 fetuses born 5070 of losses have chromosomal abnormalities Relations Between Species o Neutralism 0 Mutualism 2 organisms interact where both derive a fitness benefit increased reproductive output ResourceResource Relationship resources are exchanged usually nutrients Eg Mycorrhizae plant roots and fungi carbohydrates to fungi and phosphate and nitrogen to plant Rhizobia bacteria and plants bacteria fix nitrogen for leguminous plants and gain carbohydrates from plant Service Resource Relationship services are exchanged for resources usually nutrients Eg Pollination nectar or pollen are traded for pollen dispersal Eg Seed dispersal squirrels get nuts and nuts are dispersed ServiceService Relationship services are exchanged Eg Sea anemones and anemone fish sea anemones protect anemone fish against predators and anemone fish protect anemone against the butter y fish Faculative Mutualism the partners don t necessarily have to live together 0 Boran people of Africa and the honey guide Greater honey guide leads people to bee colonies Borans use fire and smoke to drive off the bees break open the nest and remove the honey but leave larvae and wax behind The bird gains access to larvae and wax The use of fire and smoke reduces the bird s risk of being stung and humans increase accessibility of nests 0 Eg Ants protect aphids from ladybug beetles and receive sugar water sap in return Obligate Mutualism termites and their gut agellates Threeway mutualism ants caterpillars owers owers produce nectar and get pollinated by caterpillar Caterpillar gets nectar spreads pollen and has nectar glands Ants drink nectar and protect caterpillar and ower from herbivores and predators Mutualism and Cheaters Eg Some owers don t produce pollen and pollinators can t distinguish them from those that do Eg Some cleaner fish don t just clean parasites off of their clients but sneak a bit of mucus or skin as well What is to stop this from happening o If this happens on a large scale then this can evolve into commensalism or parasitism o Competition Resource Competition Interspecific between species o Scramble competition same resource at different times moose and rabbits o Contest competition same resource at same time jackals and vultures hyenas and lions Results of Competition One species wins and the other becomes extinct Competitive Exclusion Principle complete competitors cannot coexist Gause s Principle CoeXistence shared habitat Populations are maintained below competitive levels eg In uences such as disease parasitism and predation eg African antelope and predators eg Starfish Resource partitioning when two species partition divide a resource based on behavioral or morphological variation and thereby reduce competition Habitat Partitioning eg Warblers using different parts of the tree Temporal Partitioning eg hawks and owls feed at different times of day Seasonal Partitioning eg May ies and other stream invertebrates emerge at different times of the year from the emergence times of their potential competitors Food type or foraging strategy partitioning eg large cats with antelope sit and wait vs active chase leopard and cheetah Results of Competition Resource partitioning and character 0 divergence Competition leads to extinction or coexistence Coexistence leads to shifting advantages low population density and evolution Evolution leads to extinction more competition or resource partitioning less competition Keystone Species a species that plays a critical role in maintaining the structure of an ecological community and whose impact on the community is greater than would be expected based on its relative abundance or total biomass Eg beaver transforms its territory from a stream to a pond of swamp Eg elephants destroy trees making room for the grass species Without these animals much of the savanna would turn into woodland Intraspecific within a species Predation Parastitism Commensalism Amensalism Intraspecific Competition competition between members of the same species for resources o Competition for individual survival eg food space sunlight shelter oxygen water o Competition for reproductive success Sexual Selection competition among individuals of the same sex for reproductive success 0 Male competition o Female choice 0 Different from natural selection which is a battle for survival This is a battle for reproductive rights Male Competition Breeding Rights 0 Males fighting eg elephant seals 0 Threat displays fighting should be avoided leads to sexual dimorphism o Sperm competition Fire ant 3 spermegg Honey bee 2S Human 4S0 million Horse 7 billion Pig 20 billion o Sperm removal eg insect barbed penises scoop out competitor s sperm Eg damsel y 0 Male guarding of female laying eggs eg dragon y Female Choice eg female blackbirds choose males with good territory Eg female barn swallows choose males with the longest tails o Which traits are selected for traits selected with potential for reproductive success health wealth amp power o Males are less discriminating than females males have a low cost of reproduction females have a high parental investment o Traits without apparent survival value peacock how can this happen 0 Runaway Selection 0 O O O female chooses males with fancy tails sons get fancy tails daughters get tendency to select fancy tails but why would she prefer some traits over others ones with no apparent advantage 0 How are mate preferences developed Some are learned eg imprinting in turkeys Eg eye ring in sea gulls 0 Are some preferences genetic Swordtail pllatyfish Some species with swords and some without Females of the swordtail species prefer individuals with the longest tails Is this genetic or learned Intraspecific Competition Why do individuals cooperate o Food capture gathering Predator avoidance Protection Build shelters Care giving Reproduction Altruism Kin selection a form of natural selection that favors traits that increase survival or reproduction of an individual s kin at the expense of an individual It involves altruism or self sacrifice An act by one individual that increases fitness of others at that individual s expense benefits close relatives 0 But what possible selective advantage would there be to self sacrifice for that matter any altruistic act Inclusive fitness sum of the reproductive success of individuals sharing a genotype 0 an altruistic act may increase the chances your genes will survive 0 If you save 2 brothers or sisters you will save your genes they each share 12 of your genes Individual fitness determined by the number of an individual s offspring Inclusive fitness determined by the sum total of reproductive success of all individuals sharing a genotype 0 Predators and Parasites as Selection Agents Parasites make up the majority of species on earth OOOOOOO O 0 Only 5000 species of mammals but 5000 species of tapeworms alone 200000 species of parasitic wasps Most common parasites viruses bacteria worms How do parasites affect hosts 0 O Consume energy Destroy cells obstruct functions of organs produce toxins Results of parasitism O O 0 Can kill host AIDS Malaria in uenza Can make them sick and so easier for predators to catch and easier for other parasites to infect Can change the behavior of host cough sneeze behavior improves spread of parasite Result of parasitehost interactions 0 Host can become extinct across entire range eg Chestnut blight fungus squirrel populations crashed and 5 moth species became extinct Lamprey in Great Lakes Parasite can become extinct too unless there is an alternative host Alternative hosts eg African sleeping sickness Trypanosomes carried by tse tse y Infects humans and all hoofed animals antelope pigs horses cows buffalo affects brain Identity switching to avoid immune system eg in uenza high mutation rate E g African sleeping sickness parasite switches surface proteins so immune system can t identify it Coevolution of parasite and host 0 O E g Myxoma virus and rabbits rabbits introduced into Australia in 1859 Germ Warfare against the rabbits scientists extracted myxoma virus from South American rabbits where it causes little damage except skin lesions and injected it into European rabbits Myxoma killed Australian rabbits in lab tests In the wild it is carried by mosquitoes which pick it up when they bite rabbits 0 In 1950 injected rabbits in the wild with rabbits 13 epidemic killed 99 2 epidemic killed 85 6 epidemic killed 25 today few rabbits are killed Parisitism leads to extinction or coexistence o Co existence leads to alternate hosts for parasite or identity switching for parasite or coevolution Co evolution leads to parasite becomes less devastating or host becomes more resitant Predators as Selection Agents Gause s Experiments 0 Didinium predator Paramecium prey o Effects of predation Prey becomes extinct and predator becomes extinct Predator becomes extinct and prey population explodes Predator and prey population coexist evolution is possible given time Co existence o Unstable equilibrium Short term irregular balance Temporary local extinction and re immigration Pre switching Specialized predators switching not possible 0 Pandas only eat bamboo Koalas only eat eucalyptus But pigs and humans eat almost everything Generalized predators eg European owl and meadow mole 10 different secondary food sources buffer species Predator Prey Cycles Predator kept at low populations because of other factors eg disease competition Evolutionary Arms Race between predator and prey only the best predators survive and only the best prey survive coevolution of predator and prey Avoiding Predation O Camou age by mimicry of objects praying mantis mimicking orchid blossom caterpillars mimicking plant stems Camou age by hiding resemblace to background peacock ounder mimicking surroundings Camou age by disruptive patterning ptarmigan and five chicks in Alaska Camou age by behavior leafy sea dragon fish camou aged by shape color and it sways back and forth like sea weed Camou age by countershading penguins sharks o Dazzle patterning o Batesian Mimicry n1imicking dangerous or unpalatable species 2 wasp species can look exactly the same as 3 moths and a beetle mimicking wasps o Mullerian Mimicry all species are unpalatable or dangerous and have the same color pattern tropical butter ies are all unpalatable this is a form of mutualism Co existence guppies in Trinidad o Why do guppies in the lower pools have different color patterns than in the upper pools o Hypothesis Guppies have evolved a pale color in response to selective pressure from pike predator o Test by John Endler using brightly colored guppies 10 large pools with guppies in green house 0 4 pools with guppies and pike 4 pools with guppies and killifish 2 pools with only guppies o Experiments in the field where guppies are moved between ponds show similar results 0 Predation leads to extinction or coexistence Coexistence leads to alternate prey for predator switching advantages population cycles or predator population kept low by disease or predation or coevolution Co evolution leads to prey becoming harder to catch or predator becoming more effective Speciation Species kind or type in Latin 0 Typological species each kind of organism is fixed and immutable and can be represented by an idea individual the type specimen Linnaean Nomenclature o Biological definition of species reproductively isolated group of actually interbreeding natural populations that produce fertile offspring 0 Biological species reproductve isolated populations o Sympatric species ranges overlap easy o Allopatric species ranges don t overlap hard o How can we test if two populations are two species Biological species definition used 10 of the time Morphological and chemical differences used 90 of the time 0 Problems in identifying species 0 Polymorphic species species with many different types of individuals 0 Sibling species virtually identical species 0 Ring species continuous gradual shift in phenotype over a large range The end populations can t interbreed genetic drift 0 Asexual species can t use biological species definition o Fossil species can t use biological species definition What keeps species from interbreeding o Reproductive isolating mechanisms Reproductive isolation mechanisms 0 Prezygotic barriers before zygote formation Ecological barriers share territory but occupy different regions Behavioral barriers eg temporal isolation Mechanical barriers distinct reproductive parts Gametic barriers mating occurs but egg and sperm are incompatible due to lack of interaction of receptors on the cell membranes o Post zygotic barriers after zygote formation Hybrid inviability fertilization occurs but zygote embryo or larva dies Hybrid sterility healthy hybrid unable to reproduce due to abnormal gametes eg mules 0 Populations do not strive to become species How are species formed Microevolution Mechanisms of Speciation o Allopatric Speciation geographic speciation o 2 steps geographic separation of a once continuous population reproductive isolation produced during genetic drift or natural selection o Sympatric Speciation 0 Ecological speciation speciation within a population occurring in a single habitat o Mechanism Instantanieous speciation new species formed in one generation Mutatioin not probable Polyploidy common in plants e g hybrid speciation Hybrid polyploidy eg Marsh grasses Spartina alterni ora x Spartina maritina 0 American X British Spartina townsendii Gradual speciation eg Tephritid y specializing on different host hawthorn trees Lecture 22 7 Characteristics of Life o Cellular organization Ordered complexity Sensitivity respond to stimuli Growth development and reproduction Energy utilization Homeostasis o Evolutionary adaptation 0 Origin of the Universe 0 Big Bang 137 BYA 0 All matter and energy super condensed and then a cataclysmic explosion o 13 hydrogen formed then helium formed 0 Formation of the solar system 46 billion years ago Formation of core mantle crust and atmosphere Asteroid bombardment 200 million years 0 Formation of seas lakes and rivers continents formed Oldest rocks 44 BYA 0 Evidence of even older fossils chemical fossils in Greenland 0 Chemical fossils dated 38 BYA Earth is uniquely suited for life o Right distance from the sun the temperature is right Not too hot water9 steam Not too co1d water9ice Just right water9liquid 0 Right size and density so the gravity is right Not too sma1l atmosphere Not too 1arge atmosphere down Just right atmosphere with sunlight penetration Formation of Life o Hypotheses on origin Divine Creation Spore Theory Panspermia Directed panspermia aliens Originated on Earth Spontaneous Generation o Spalanzini s experiment o Pasteur s experiment Primary abiogenesis Life came from inorganic chemicals Oparin and Haldane OOOOO 0 Chemical Evolution o 1 Inorganic chemicals 0 2 Organic chemicals 0 3 Interacting chemical systems reactions Biological Evolution 0 4 Reproducing molecules o 5 Cells o 6 Multicellular organisms Experimental Evidence o Miller and Urey s experiments 1953 and 1959 o Note gasses H20 NH3 CH4 H2 Miller and Urey s Experiments 0 O O O Produced several organic molecules including amino acids Many other gas mixtures produce similar products Organic soup Titan Saturn s largest moon has atmosphere of methane nitrogen and carbon monoxide Scientists bombarded this atmosphere in the lab with radio frequency radiation and produced amino acids and all of the nucleotides of DNA and RNA without the presence of water Simple organic molecules have been detected in space 130 molecules detected including Ammonia Methane Acetylene Formaldehyde Glycolaldehyde Anthracene Pyrene Meteorites have simple organic molecules Conclusion It is easy to produce organic molecules from inorganic molecules Hypothesis is supported Polymerization experiments Simple sugars9Complex carbohydrates Amino acids proteins Nucleotides9Nucleic acids Fatty acids9Lipids and Glycerol Polymerization can be accomplished easily by Evaporation Freezing Heating Adsorption onto minerals and clays with catalytic properties hypothesis is supported Interacting chemical systems Coaceryates colloidal drops of organic materials in solution oparin Coacervate Properties Feeding Size of small cell Membrane Add enzymes molecular reactions Growth and division Reproduction DNA and RNA both make copies of themselves using nuc1eotides feeding and reproduction Competition for raw materials between molecules surviVal of the fittest and natural selection
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