On your Notecards please write the following: (1) Name (2) Year (3) Major (4) Courses taken in Biology (4) Career goals (5) Email address (6) Why am I taking this class?
The Unifying Concept in Biology Evolution 410 11/27/2018 EVOLUTION The Unifying Concept in Biology Dr. Carol Eunmi Lee University of Wisconsin, Madison Professor Carol Lee
Theodosius Dobzhansky (1900-1975) Evolution 410 11/27/2018 “Nothing in biology makes sense except in the light of evolution” Theodosius Dobzhansky (1900-1975) Professor Carol Lee
Reading (1) Evolutionary Analysis 5th Edition 11/27/2018 Reading (1) Evolutionary Analysis 5th Edition Jon Herron & Scott Freeman (2) Journal articles posted on Course Website: http://carollee.labs.wisc.edu/Evolution410.html Professor Carol Lee
Who am I? BA, MA from Stanford University Evolution 410 11/27/2018 Who am I? BA, MA from Stanford University Anthropology (Human Evolution) PhD, University of Washington Evolutionary Genetics Postdoc, University of California, San Diego Evolutionary Physiology and Biochemistry Professor, University of Wisconsin, Madison Center of Rapid Evolution, Integrative Biology, Genetics Professor Carol Lee
Evolution 410 11/27/2018 Research in my Lab Adaptation, Functional Evolutionary Genomics, Physiological Evolution Rapid evolution of invasive species entering the Great Lakes (zebra mussels, quagga mussels, copepods) Evolution of waterborne infectious diseases carried by these invaders (cholera) Arthropod Genome Evolution Professor Carol Lee
TA Juanita Diaz Background in Geology and Evolutionary Biology 11/27/2018 TA Juanita Diaz Background in Geology and Evolutionary Biology Will lead discussion starting this week (times posted on website) Office Hours: Wed 12:00-2:00 pm, Birge Hall, Room 421 Professor Carol Lee
Course Website: http://carollee.labs.wisc.edu/Evolution410.html
Background needed for this course Some understanding of basic genetics (Hardy Weinberg Equilibrium, DNA, RNA, transcription, translation, allele, genotype) Please review your Introductory Biology text on basic Genetics
OUTLINE: 1) Overview 2) What is Evolution? 3) Basic Concepts 11/27/2018 OUTLINE: 1) Overview 2) What is Evolution? 3) Basic Concepts 3) Practical Applications 4) Example of Evolution in Action: Evolution of HIV Professor Carol Lee
Course Overview (1) TODAY: What is Evolution? Practical Applications 11/27/2018 (1) TODAY: What is Evolution? Practical Applications (2, 3) History of Evolutionary Thought (4) Hardy Weinberg Equilibrium (no evolution), Genetic Drift (5) EVOLUTIONARY MECHANISMS: Genetic Drift (6, 7, 8) EVOLUTIONARY MECHANISMS: Genetic Variation (9) EVOLUTIONARY MECHANISMS: Epigenetic Inheritance (10,11,12) EVOLUTIONARY MECHANISMS: Natural Selection (13) Adaptation vs. Plasticity (14) Evolutionary Tradeoffs (Aging) (15, 16) Molecular Evolution (17) Genome Evolution (18, 19) Speciation (20) Earth History, History of Life on Earth (21) Reconstructing the Tree of Life (23) Plant Evolution (24) Animal Evolution (25, 26) Human Evolution Course Overview Professor Carol Lee
Structure of Lectures: Evolution 410 11/27/2018 Introduction What is Evolution? History of Evolutionary Thought No Evolution Hardy Weinberg Equilibrium Evolutionary Genetic Drift Mechanisms Genetic Variation (Mutation, Recombination) Epigenetic Variation Natural Selection (including molecular and genome levels) Molecular Evolution Regulatory Evolution Amino Acid Evolution Evolution of Genome Architecture Macroevolution Speciation History of Life on Earth Tree of Life Diversity Plant Evolution Animal Diversity Human Evolution Professor Carol Lee
Evolution 410 11/27/2018 Assignments & Exams • 3 exams of equal weight, multiple choice: 100 points each = 300 pts total • 3 quizzes: 30 points each = 90 pts total • 3 Homeworks: 210 pts total Professor Carol Lee
Q: What is Evolution? Q: How does Evolution Occur? 11/27/2018 Q: What is Evolution? Q: How does Evolution Occur? These are potential exam questions Professor Carol Lee
Q1: What is Evolution? This question will be on the final exam 11/27/2018 Q1: What is Evolution? This question will be on the final exam Professor Carol Lee
Q1: What is Evolution? (give the most comprehensive answer) 11/27/2018 Q1: What is Evolution? (give the most comprehensive answer) The increase in fitness over time due to natural selection, or adaptation The accumulation of mutations, which alter fitness over time The change in allele frequencies (or the heritable expression of those alleles) in a population across generations The progression into more complex forms of life This question will be on the final exam Professor Carol Lee
Evolution 410 11/27/2018 Q: What is Evolution? Change in proportions of genetically different individuals at each generation Leading to an average change in characteristics of populations over time change in allele frequencies (genetic composition) or the heritable change in the expression of those alleles (epigenetic inheritance) Acts by removing individuals from the population, or by allowing some to leave more offspring By population, we are referring to a group of interbreeding individuals and their offspring (in the case of sexual species) This will be on the exam Evolution is a statistical process Many prominent evolutionary biologists are mathematicians or statisticians It is the statistical change in proportions of individuals in a population Acts on individuals that consequently end up with different fitnesses Professor Carol Lee
Q1: What is Evolution? (give the most comprehensive answer) 11/27/2018 Q1: What is Evolution? (give the most comprehensive answer) The increase in fitness over time due to natural selection, or adaptation The accumulation of mutations, which alter fitness over time The change in allele frequencies (or the heritable expression of those alleles) in a population across generations The progression into more complex forms of life This question will be on the final exam Professor Carol Lee
Q1: What is Evolution? (give the most comprehensive answer) 11/27/2018 Q1: What is Evolution? (give the most comprehensive answer) The change in allele frequencies (or the heritable expression of those alleles) in a population across generations. (BB) (Bb) (bb) Blue Purple Red Generation 1: 250 500 250 Generation 2: 200 600 200 Generation 3: 100 800 100 Here the frequencies of the B and b alleles remain the same across generations, the population has gone out of Hardy Weinberg Equilibrium, and is evolving… Although, even if allele frequencies in a population remain the same across generations, a population is evolving if it goes out of Hardy-Weinberg Equilibrium Professor Carol Lee
Q1: What is Evolution? (give the most comprehensive answer) 11/27/2018 Q1: What is Evolution? (give the most comprehensive answer) The change in allele frequencies (or the heritable expression of those alleles) in a population across generations. (BB) (Bb) (bb) Blue Purple Red Generation 1: 250 500 250 Generation 2: 200 600 200 Generation 3: 100 800 100 Here the frequencies of the B and b alleles remain the same across generations, the population has gone out of Hardy Weinberg Equilibrium, and is evolving… Although, even if allele frequencies in a population remain the same across generations, a population is evolving if it goes out of Hardy-Weinberg Equilibrium genotype frequencies should follow HW expectations, given the allele frequencies Professor Carol Lee
Q3: How does Evolution Occur? 11/27/2018 Q3: How does Evolution Occur? So Evolution acts through Genetic Drift or Natural Selection acting on the genetic variation caused by mutations or recombination, or lack of variation caused by inbreeding Professor Carol Lee
Q3: How does Evolution Occur? Biology 151, Evolution 11/27/2018 Q3: How does Evolution Occur? ***Through 5 Major Mechanisms: Genetic Drift Mutation Heritable Epigenetic Modification Migration Natural Selection (Think about what forces would change the allele frequencies in a population, or the heritable expression of those alleles) So Evolution acts through Genetic Drift or Natural Selection acting on the genetic variation caused by mutations or recombination, or lack of variation caused by inbreeding Professor Carol Lee
i.e. what causes changes in the allelic composition in a population? Biology 151, Evolution 11/27/2018 i.e. what causes changes in the allelic composition in a population? Genetic Drift: totally random changes in allele frequency from generation to generation Mutation: changes in the genetic code, such as errors in DNA replication, gene deletions or duplications, etc… Epigenetic Inheritance: heritable changes that are not due to changes in DNA sequence itself, but the expression of the DNA, such as changes in DNA methylation and histone modifications, etc…changes “epi-alleles” not the genetic code (actual alleles) Migration: alleles moving from one population to another Natural Selection: when some alleles favored over others due to an increase in fitness (not random); acts on genetic variation in the population So Evolution acts through Genetic Drift or Natural Selection acting on the genetic variation caused by mutations or recombination, or lack of variation caused by inbreeding Professor Carol Lee
Natural Selection Sources of Genetic Variation Biology 151, Evolution 11/27/2018 Sources of Genetic Variation Mutation generates genetic variation Epigenetic Inheritance changes expression of genes Genetic Drift reduces genetic variation Natural Selection Natural Selection acts on genetic or epigenetic variation in a population Without genetic or epigenetic variation, Natural Selection cannot occur Professor Carol Lee
Evolutionary Concepts Permeate all Aspects of Biology 11/27/2018 Evolutionary Concepts Permeate all Aspects of Biology Biotechnology Agriculture Medicine Conservation Professor Carol Lee
Evolution 410 11/27/2018 Agriculture Most of your food is a product of intense artificial selection, or human induced evolution Professor Carol Lee
Human-induced Evolution
Evolution of a Pathogen as an Example: 11/27/2018 Evolution of a Pathogen as an Example: I will now use an infectious disease to illustrate basic evolutionary concepts. The following example illustrates several evolutionary mechanisms I will explain these concepts in more detail over the next few lectures Professor Carol Lee
HIV infects macrophages, T-cells Evolution 410 11/27/2018 HIV: Fastest evolving organism on Earth HIV infects macrophages, T-cells Professor Carol Lee
Biology 151, Evolution 11/27/2018 HIV Facts AIDS is among the most deadly epidemics in Human History (1981-2012: ~36 million deaths) ~78 million have been infected, ~36.7 million people currently living with AIDS (estimated 2015) 90 million deaths predicted by 2020 UNAIDS. 2016 Report on the Global AIDS Epidemic (http://www.unaids.org/sites/default/files/media_asset/2016-prevention-gap-report_en.pdf) #people living with HIV Professor Carol Lee
Evolution 410 11/27/2018 Professor Carol Lee
Evolution 410 11/27/2018 Problem : HIV has the fastest mutation rate of any virus or organism observed to date HIV evolves more rapidly than humans, and more quickly than the ability of humans to produce new drugs Implications: AIDS vaccines are unlikely to work on all strains of the virus… …and unlikely to work on a given strain in the long run Our understanding of how to combat viruses had in general been poor, and the recent intensive research on HIV has greatly enhanced our understanding of how to combat viruses in general Professor Carol Lee
HIV Retrovirus with two single strand RNA genomes Biology 151, Evolution 11/27/2018 HIV Retrovirus with two single strand RNA genomes Uses the enzyme Reverse Transcriptase to replicate RNA → DNA Attacks host immune system: infects macrophages and helper T cells Professor Carol Lee
How might HIV Evolve? (1) Drugs impose Selection on HIV: Biology 151, Evolution 11/27/2018 (1) Drugs impose Selection on HIV: → evolution of drug resistance (2) Transmission Rate imposes Selection on HIV: → evolution of virulence (3) Host immune system also imposes selection on the virus HIV → will not discuss Professor Carol Lee
(1) Natural Selection in Response to Drugs Biology 151, Evolution (1) Natural Selection in Response to Drugs 11/27/2018 Example of an HIV Drug: AZT AZT (Azidothymidine) is a thymidine mimic which stops reverse transcription and impedes viral replication Professor Carol Lee
Why does AZT work initially but fail in the long run? Evolution 410 11/27/2018 FAST MUTATION RATE: Lots of Mutations arise, including in the viral reverse transcriptase gene genetic variation NATURAL SELECTION favors reverse transcriptase enzyme mutant that can recognize AZT and not use it (meaning the ones with the mutant now live, the others die) The careful reverse transcriptase enzyme is slow, but the virus is now resistant to AZT (Tradeoff between fast & sloppy vs. slow & careful enzyme) What would happen when AZT therapy stops? AZT AZT: where the nucleotide thymidine has a hydroxyl group, AZT has an azide group, so nucleotides cannot be added on during DNA synthesis… blocking reverse transcription (the synthesis of DNA from the viral RNA genome) natural selection refers to who lives and who dies because of their genetic composition Professor Carol Lee
Evolution 410 Population of HIV individuals with different reverse transcriptase variants In the presence of AZT, Natural Selection favors mutants that are resistant to AZT (blue, have slow & careful enzyme) Results in %change in the population, toward higher % of AZT resistant mutants Figure 1.14 How HIV populations evolve resistance to AZT Variation due to mutation, inheritance, and differences in survival due to AZT results in a change in the composition of the population over time. Time Professor Carol Lee
So, what would happen when AZT therapy stops?
(2) Selection on Virulence of HIV Biology 151, Evolution 11/27/2018 Need to keep host alive long enough to get passed on to the next host (Evolutionary Tradeoff between fast viral population growth versus keeping the host alive) High Transmission rate : High Virulence (Can grow fast and jump to the next host; ok if host dies; the genetic strain that grows faster will win) Low Transmission Rate : Low Virulence (More virulent strains would die with the host and get selected out; less virulent strain that does not kill the host will win) Professor Carol Lee
Selection on Virulence Biology 151, Evolution 11/27/2018 Selection on Virulence High Transmission Rate: will select for High Virulence Professor Carol Lee
High Transmission Rate Biology 151, Evolution 11/27/2018 High Transmission Rate If the virus is likely to move to a new host, the faster growing (and more virulent) strain is likely to overtake the slower strains and “win” It’s ok to kill the host, since the chances of jumping to a new host is high Natural selection will favor the MORE virulent strain Professor Carol Lee
Selection on Virulence Biology 151, Evolution 11/27/2018 Selection on Virulence Low Transmission Rate: will select for Low Virulence Professor Carol Lee
Biology 151, Evolution 11/27/2018 Low Transmission Rate If the virus is not likely to move to a new host the slower growing (and less virulent) strain is likely to “win” It’s not ok to kill the host, since the chances of jumping to a new host is low. If the virus kills the host, it will kill itself Natural selection will favor the LESS virulent strain Professor Carol Lee
So, how would you select for a less harmful strain of HIV?
Evolution 410 11/27/2018 Combating HIV Must lower transmission rate of HIV so that less fatal strains evolve Must understand evolutionary properties of a disease: Evolutionary history Mutation rate Selective Forces Evolutionary Tradeoffs Evolution in response to drug AZT: slow & accurate vs. fast & sloppy replication Evolution in response to transmission rate: slow growing & less virulent (keep host alive) vs. fast growing & more virulent Professor Carol Lee
Evolution in Host-Parasite System 11/27/2018 Evolution in Host-Parasite System SELECTION ON THE HOST (Humans) Some humans have resistance to some HIV strains. Proportion of people with resistant alleles is increasing in some populations. Gene Therapy? Could we win an arms race? But HIV evolves faster than we do and more quickly than our ability to produce new drugs Professor Carol Lee
Why does AZT work initially but fail in the long run? Evolution 410 11/27/2018 FAST MUTATION RATE: Mutations in the viral reverse transcriptase gene of HIV arises NATURAL SELECTION favors reverse transcriptase enzyme that can recognize AZT and not use it These mutations slow down the virus (as it becomes more careful), but makes the virus resistant to AZT (Tradeoff between speed vs. accuracy of reverse transcription) What would happen when AZT therapy stops? Back mutations that restore the Amino Acid sequence to the original state are then favored by selection so that reverse transcription could speed up again (fast & sloppy are favored – because fast replicating mutants would outgrow the slower) AZT AZT: where the nucleotide thymidine has a hydroxyl group, AZT has an azide group, so nucleotides cannot be added on during DNA synthesis… blocking reverse transcription (the synthesis of DNA from the viral RNA genome) Professor Carol Lee
Questions: (1) What is Evolution? 11/27/2018 Questions: (1) What is Evolution? (2) How does evolution operate? What are the main Evolutionary Mechanisms? (3) Discuss how an understanding of evolution impacts practices in Agriculture, Medicine, and Conservation (4) For example, discuss how different evolutionary mechanisms impact the evolution of HIV, the virus that causes AIDS Professor Carol Lee
Concepts Evolution Population Genetic Drift Natural Selection Mutation 11/27/2018 Concepts Evolution Population Genetic Drift Natural Selection Mutation Genetic Variation Allele, Genotype HIV Professor Carol Lee