Download Phylogenetics: Understanding the Basics of Molecular Phylogenetics and Tree Building - Pro and more Lab Reports Bioinformatics in PDF only on Docsity! #29 - Phylogenetics 10/31/07 BCB 444/544 Fall 07 Dobbs 1 1BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 BCB 444/544 Lecture 29 Phylogenetics #29_Oct31 2BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Mon Oct 29- Lecture 28 Promoter & Regulatory Element Prediction • Chp 9 - pp 113 - 126 Wed Oct 30 - Lecture 29 Phylogenetics Basics • Chp 10 - pp 127 - 141 Thurs Oct 31 - Lab 9 Gene & Regulatory Element Prediction Fri Oct 30 - Lecture 29 Phylogenetic Tree Construction Methods & Programs • Chp 11 - pp 142 - 169 Required Reading (before lecture) 3BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Assignments & Announcements Mon Oct 29 - HW#5 HW#5 = Hands-on exercises with phylogenetics and tree-building software Due: Mon Nov 5 (not Fri Nov 1 as previously posted) 4BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 BCB 544 "Team" Projects Last week of classes will be devoted to Projects • Written reports due: • Mon Dec 3 (no class that day) • Oral presentations (20-30') will be: • Wed-Fri Dec 5,6,7 • 1 or 2 teams will present during each class period See Guidelines for Projects posted online 5BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 BCB 544 Only: New Homework Assignment 544 Extra#2 Due: √PART 1 - ASAP PART 2 - meeting prior to 5 PM Fri Nov 2 Part 1 - Brief outline of Project, email to Drena & Michael after response/approval, then: Part 2 - More detailed outline of project Read a few papers and summarize status of problem Schedule meeting with Drena & Michael to discuss ideas 6BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Seminars this Week BCB List of URLs for Seminars related to Bioinformatics: http://www.bcb.iastate.edu/seminars/index.html • Nov 1 Thurs - BBMB Seminar 4:10 in 1414 MBB • Todd Yeates UCLA TBA -something cool about structure and evolution? • Nov 2 Fri - BCB Faculty Seminar 2:10 in 102 ScI • Bob Jernigan BBMB, ISU • Control of Protein Motions by Structure #29 - Phylogenetics 10/31/07 BCB 444/544 Fall 07 Dobbs 2 7BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Chp 10 - Phylogenetics SECTION IV MOLECULAR PHYLOGENETICS Xiong: Chp 10 Phylogenetics Basics • Evolution and Phylogenetics • Terminology • Gene Phylogeny vs. Species Phylogeny • Forms of Tree Representation • Why Finding a True Tree is Dificult • Procedure of Building a Phylogenetic Tree 8BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Evolution and Phylogenetics • Evolution – the development of biological form from other preexisting forms • Evolution proceeds by natural selection 9BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Natural Selection • Species can produce more offspring than the environment can support. This leads to competition for resources. Genetic variations exist in a population that give some individuals an advantage, others a disadvantage, leading to differential reproductive success. 10BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Phylogenetics • Phylogenetics is the study of the evolutionary history of living organisms • Uses tree like diagrams to represent the pedigrees of the organisms • Similarities and differences seen in a multiple sequence alignment are easier to make sense of in a phylogenetic tree 11BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Data Used in Phylogenetics • Fossil records - morphology and timeline of divergence • Limitations - not available for all species in all areas, morphology determined by multiple genetic factors, fossils for microorganisms are especially rare • Molecular data - DNA and protein sequences - molecular fossils • Advantages - lots of data, easy to obtain • Limitations - can be difficult to get sequences from extinct species • Physical, behavior, and developmental characteristics can also be used in phylogenetics 12BCB 444/544 F07 ISU Terribilini #29- Phylogenetics 10/31/07 Molecular Phylogenetics • Molecular phylogenetics is the study of evolutionary relationships of genes and other biological macromolecules by analyzing their sequences • Sequence similarity can be used to infer evolutionary relationships
