L1 Slides - Intro-2 - Organic Evolution PDF

Welcome to Organic Evolution! (PCB4674 with Dr. Yusan Yang) If this is not your class, now’s the time to run!  Today’s Plan Get to know your Instructor and TA Syllabus and Logistics Lecture 01 Introduction to Evolutionary Biology  Get to know...

Welcome to Organic Evolution! (PCB4674 with Dr. Yusan Yang) If this is not your class, now’s the time to run!  Today’s Plan Get to know your Instructor and TA Syllabus and Logistics Lecture 01 Introduction to Evolutionary Biology  Get to know your instructor! Yusan Yang (楊⾬珊), Ph.D. (yes, the color matching Email: [email protected] is intentional) Office hours: Mon 3:00-4:00pm SCA126 (or by appointment if you can’t make it) Courses: Evolution, Animal Behavior Lab: https://yusanyang.wordpress.com  Postdoc PhD Year 1 Washington University in St. Louis Tulane University, New Orleans PhD Year 2-6 University of Pittsburgh Research Intern National Institute of Genetics, Japan St. Louis Pittsburgh Mishima, Japan New Orleans Tampa Taipei, Taiwan Panama Assistant Professor University of South Florida PhD Field site Undergrad Smithsonian Tropical Research Institute, Panama National Taiwan University Evolution of Color and Behavior in Color Polymorphic Frogs https://youtu.be/9TlVCXegmMw?t=14  Get to know your TA! Lauren Walling, M.S. Email: [email protected] Office hours: Wed 10:00-11:00 am SCA 224 (or by appointment if you can’t make it) Past Research & Education Bachelor's degree from University of Illinois Urbana- Champaign Lab tech in laboratory that studied the spread of Chronic Wasting Disease in White Tailed Deer Master’s degree from University of Louisiana at Lafayette Thesis was on DNA methylation in Octocorals Completed many hours of annotating deep-sea dives NOAA 2015 Hohonu Moana  Current Research Doctoral degree from University of South Florida! Started Fall 2021 Working on dissertation determining: o how DNA methylation is affected by heat/cold exposure in coral symbionts. o If DNA methylation is affected by symbiont status o If there is a correlation between invasive Spartina (seagrass) populations and their DNA pattern  Today’s Plan Get to know your Instructor and TA Syllabus and Logistics Lecture 01 Introduction to Evolutionary Biology COURSE SCHEDULE 4 Units: Foundations Evolutionary Genetics Studying Adaptation Macroevolution & Human Evolution Each with: 5-6 lectures 2 homework 1 Discussion (except U1) 1 Exam 1Homework is opened on the indicated date, and due the Sunday 23:59 of the weekend Grade Breakdown  Participation (20%) This will include 1-2 graded questions on the previous lecture beginning of each class, and a few ungraded questions during. 2 pts for answering, 1 pt for correctness Assignment Goals: review contents of the previous lectures assess comprehension of the material just discussed reflect on concepts before we fully cover them in class.  In Class Discussion (15%) 1. Individual homework (10 pts): Read the paper and complete worksheet before class time. Upload to Canvas (graded for completeness). 2. Group discussion (10 pts): bring your completed homework to class, and work in groups on a group worksheet. Turn in the group worksheet at the end of the class (graded for correctness). (I will pick groups for you, and you will be grouped with different people in the three discussions) Assignment goals: reading scientific papers, science communication, real world applications Homework (20%) Canvas quiz, 10-15 MC questions No time limit; each homework can be taken twice. Assignment goals: Stay on top of the materials, identify gaps, practice for exam style questions. Tips: Homework/Discussion prep are opened for several days. Plan ahead and don’t wait till the last minute!  Midterms (30%) and Final (15%) Midterm exams (30%): 3 midterms (dropping lowest). 75 min, paper test 1 essay question – 10 pts 1 extra credit essay question (+5 pts) 30 multiple choice questions (3 pts each) – 90 pts Final exam (15%): Cumulative, no dropping 120 min, paper test 2 essay question – 10 pts 1 extra credit essay question (+5 pts) 30 multiple choice questions (3 pts each) – 90 pts  Textbook Optional Lectures are loosely based off the chapter contents, but I will add or skip contents Reading can reinforce understanding of concepts, or provide a different option of learning. You will not be tested on material that we do not discuss during lecture, but I might test you on a concept we covered using an example described in the textbook. © 2014 Pearson Education, Inc.  Lecture Handouts Study guide Lecture slides © 2014 Pearson Education, Inc.  What to expect in this course There will be lots of results interpretation, graph reading, and knowledge applications. Science literacy: The ability to judge the quality of scientific data and make informed decisions is a main skill that I want you to walk away from this course with.  What to expect in this course There will be human interactions (e.g. group discussion, think-pair-share) Peer learning/active learning has been proven to be more effective than passive learning, although students may not like it/think it is useful. Some data from the Integrative Biology department: students in the active/peer learning group improve more in grades/learning outcomes, but gave lower teaching evaluations than the control group.  How to succeed in this course 1. Check Canvas/emails daily for announcements. 2. Stay on top of the materials from the beginning! It’s a lot and cramming everything into one session is likely not going to work well. Spread it out and stick to a schedule. Homework schedule is designed to help you with this. 3. Attend and be engaged in lectures. Clicker questions and think-pair share are designed to help you with this. Ask questions - if something is unclear to you, it is likely unclear to someone else. There are no stupid questions. 4. Keep the learning objectives and the large picture in mind when studying; don’t just read from front to back. Study guides are designed to help with this. 5. Work to understand the concepts, not just memorize. Being able to apply and link concepts across lectures and units is important for effective learning. Office hours and studying with others are great for longer discussion of difficult concepts. PSA: read the syllabus! Questions, Comments, Concerns, etc? Let’s deal with iClicker We will start grading in-class participation on Wednesday, 8/28/24 Either physical clickers or app works! Base Frequency is “CD” (for Charles Darwin) This link should help with registration: https://www.iclicker.com/students/ Our class is called “FA24 Organic Evolution (Yang)”  Mock session - Clicker Question When is your birthday? A) Jan – Mar B) Apr – Jun C) Jul – Sept D) Oct - Dec  Mock session - Clicker Question Did you bring your iClicker device today? A) Yes B) No  First day attendance question I am using this one question Canvas quiz to satisfy USF's first-day attendance requirement. Submit your answer by the end of today to remain in the course! How would you define biological evolution if asked by a fellow scientist? What about if asked by a five-year-old?  Lecture 01 Introduction to Evolutionary Biology © 2014 Pearson Education, Inc.  Learning Objectives Explain what evolution is, and how it can be used to address questions in biology. Define the four key elements of evolution: common ancestry, microevolution, speciation, and macroevolution. Describe the major lines of evidence for evolution, giving examples of each. Evolution is the Unifying Theory in Biology  Example: What makes nature diverse? Ecological Niche: diverse habitats drive species to adapt and coexist. Divergence: Populations become different because of adaptation or drift (i.e. random chance). Speciation: Divergent populations stopped being able to exchange genes, becoming different species https://geographicbook.com/biomes-in-biogeography/  Example: Why are whales like this? Whales are mammals because they have mammary glands (phylogeny). Fossils suggest that the ancestor of whales is a land mammal. Whales have a body shape that is suited for moving in water (adaptation). Whales can hold their breath for a long time, but they can’t breathe in water (evolutionary constraint). https://www.nyit.edu/medicine/ambulocetus_natans/ Karim Iliya  Example: How did we get agricultural crops? Artificial selection: Humans choose specific traits in organisms (e.g., size, color, or yield) and breed individuals that exhibit those traits. https://biologydictionary.net/artificial-selection/ Example: Why do we need new vaccines each season? Vaccines are weakened antigens that prime our immune system to produce antibodies when we encounter the pathogen with similar surface protein. Mutations in viral surface protein can make it harder for the antibodies to bind to it, and thus reproduces more quickly (natural selection). SARS-CoV-2 VARIANT WAVES Vaccines with updated version of antigens is thus needed to keep up the arms race. https://www.nature.com/articles/d41586-021-03694-x  Acceptance of Evolution is low among the general public 2006 survey; 34 countries; 1000 respondents on average “True or False? Human beings, as we know them today, developed from earlier species of animals.” © 2014 Pearson Education, Inc. …but the trend is upward. the 4 key elements of evolutionary theory Common Ancestry: all life forms are related Microevolution: traits in a population can change from one generation to the next (e.g. beak size increases after a drought year) Speciation: lineages may diverge and split, giving rise to new species Macroevolution: New life forms can derive from earlier forms (e.g. tetrapods arose from a lineage of fish)  Think-Pair-Share How would you convince someone that doesn’t believe in/is unsure about evolution? What evidence can you use to support your statements? How do we know that… 1. all life forms are related, even drastically different ones? 2. traits can evolve over time? 3. new species come from splitting of older species?  Evidence for Common Ancestry Structural homology: Similarity in composition despite differences in function, suggesting that these species share common ancestry These appendages are called homologous structures © 2014 Pearson Education, Inc.  Evidence for Common Ancestry Molecular homology: Almost all species share how the information are coded in their DNA. Similar sequences are found in drastically different animals. https://open.lib.umn.edu/evolutionbiology/chapter/5-8-using-the-genetic-code-2/ © 2014 Pearson Education, Inc.  Evidence for Common Ancestry Vestigial structures: a useless or rudimental body part that has function in another closely related species; “bad/useless designs” Arrector pili Coccyx Appendix (muscle that cause goosebumps) https://www.niddk.nih.gov/health-information/digestive-diseases/appendicitis/definition-facts  Evidence for Microevolution Selective Breeding: in many domesticated animals and plants, distinctive varieties came from common stock, and artificial selection can change characteristics over time Paul D Stewart Darwin began studying and breeding pigeons in 1856, 3 years before publishing “On the Origin of Species” © 2014 Pearson Education, Inc.  Evidence for Microevolution Observation of Natural Populations: microevolution can occur fast enough that we can observe as populations evolve A drought happened in 1977, reducing the available seeds A hard to crack seed becomes a key food item Finch beak average in the population increase after the drought © 2014 Pearson Education, Inc.  Evidence for Speciation Laboratory Experiments: Speciation in action https://commons.wikimedia.org/wiki/File:Drosophila_speciation_experiment.svg  Evidence for Speciation Natural populations: Populations representing the process of ongoing speciation © 2014 Pearson Education, Inc.  Evidence for Macroevolution Transitional fossil: extinct species displaying mixture of traits of existing organisms. Sometimes even predicted before they were found. Archaeopteryx: found shortly after Darwin published “On the Origin of Species © 2014 Pearson Education, Inc.  Evidence for Macroevolution Transitional fossil: extinct species displaying mixture of traits of existing organisms. Sometimes even predicted before they were found. © 2014 Pearson Education, Inc.  Evidence for Macroevolution Rule of Succession: Fossils and living organisms from the same geographic area resemble each other fossil glyptodont armadillo © 2014 Pearson Education, Inc. fossil marsupial wombat  Evidence for Macroevolution Biogeography: the study of the distribution of living organisms Distribution of taxa can be explained by geographic history https://johnflo.weebly.com/biogeography.html https://en.wikipedia.org/wiki/Marsupial https://open.lib.umn.edu/evolutionbiology/  Learning Objectives Explain what evolution is, and how it can be used to address questions in biology. Define the four key elements of evolution: common ancestry, microevolution, speciation, and macroevolution. Describe the major lines of evidence for evolution, giving examples of each. Questions, Comments, Concerns, etc? Exit Poll