(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise
|
|
- Kerry Baker
- 5 years ago
- Views:
Transcription
1 Bot 421/521 PHYLOGENETIC ANALYSIS I. Origins A. Hennig 1950 (German edition) Phylogenetic Systematics 1966 B. Zimmerman (Germany, 1930 s) C. Wagner (Michigan, ) II. Characters and character states e.g. character = flower color character states = red, white, blue A. qualitative 1. multistate (red,white,blue) 2. binary (presence/absence) B. quantitative 1. continuous (measurements) 2. discontinuous (counts) C. delimitation of character states (Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise e.g. compare two char. states: linear to lanceolate / ovate (used in a cladistic analysis) vs. linear-lanceolate / lanceolate / lanceolate to narrowly ovate / lanceolate-ovate / lanceolate to broadly ovate (used in species descriptions) 2. character states should be delimited by carefully analyzed discontinuities (not necessarily absolute gaps) a. mean or range
2 b. sample size c. scoring intermediates as polymorphic for more info: Kornet, DJ and H Turner Coding polymorphisms for phylogeny reconstruction. Syst. Biol. 48: explicit justification should be given does Cladistics = Phylogenetics? clados = branch III. The distribution of character states morph = character state apo = derived plesio = ancestral syn, sym = shared auto = unique e.g. synapomorphy symplesiomorphy autapomorphy IV. The description of groups A. monophyletic = an ancestor and all of its descendants, i.e. a clade identified by synapomorphies B. polyphyletic = a group with two or more ancestral sources in which parallel similarities have evolved mistakenly grouped by homoplasy C. paraphyletic = a group including a common ancestor and some, but not all of its descendents
3 V. Polarization A. used to "root" a network B. outgroup(s) must have separated from the ingroup lineage before the ingroup diversified C. used to "infer" ancestral char. states D. current algorithms do not require a priori rooting VI. Tree construction Parsimony minimizes the number of character state changes on a tree = Hennig's auxilliary principle: "never assume convergent or parallel evolution; always assume homology in the absence of evidence to the contrary" = Ockham's Razor; (William of Ockham, 1347) or the principle of simplicity VII. Summarizing trees bird & bat example A. Consensus tree = summarizes clades found in 2 or more trees VIII. Weighting 1. strict = only clades common to all trees 2. majority rule = clades that appear in 50% or more of the trees 3. semi-strict = all clades not contradicted in other trees A. Character states 1. ordered or Wagner parsimony
4 unordered or Fitch parsimony 3. Dollo parsimony gains count for more than losses can be generalized, e.g. making losses more probable than gains B. Characters A priori weighting discouraged 2. Successive weighting is a posteriori gives homoplastic characters less weight IX. Do we believe the tree? A. Tree Statistics 1. tree length 2. consistency index CI = m / s m = minimum # of steps / character s = observed # of steps / character
5 e.g. 8/10 = 0.80 homoplasy index HI = 1 - CI a. inflated by autapomorphies (uninformative characters) b. trees with more taxa tend to have lower CI 3. retention index RI = g - s / g - m g = maximum # of steps / character a. varies between 0 and 1 e.g. (14-10) / (14-8) = 0.67 b. rescaled CI = RI X CI e.g. (0.67)*(0.8) = 0.53 B. Bootstrap Felsenstein (1985) taxa X characters matrix resampled with replication creating a pseudosample 100 [or more] pseudosamples re-analyzed resulting trees combined in a majority rule consensus tree results: % of trees that a particular clade appears in NOT a confidence interval, rather: an indication of the degree of support for a particular clade an empirical study suggests that 70 % bootstrap and above has a 95% probability of being accurate Hillis,DM; Bull,JJ; White,ME; Badgett,MR; Molineux,IJ (1992): Experimental phylogenetics: generation of a known phylogeny. Science 255: Hillis,DM; Bull,JJ (1993): An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42: C. Decay index
6 when does a clade collapse? D. Have we found the shortest tree(s)? 5 taxa = 15 unrooted trees 1. Immense numbers of trees 2. Efficiency of search algorithms 7 taxa = 945 unrooted trees 10 taxa = 2 X 10 6 unrooted trees 20 taxa = 2 X unrooted trees T B(T) = (2i-5) i=3 T terminal nodes (=taxa) i = multiply for each taxon (starting at 3) adding a root increases # by a factor of 2T-3 Search options: branch and bround & exhaustive searches: guaranteed to find the shortest tree vs. heuristic searches faster, but susceptible to "local optima" stepwise addition sequence options: random [ times], closest, simple swap options: tree-bisection reconnection subtree pruning and regrafting TBR SPR
7 nearest neighbor interchange NNI X. Applications A. Mapping characters on trees B. Biogeography C. Phylogenetic Classification 1. named groups are monophyletic 2. not all clades are named 3. criteria a. strength of evidence supporting a particular clade b. obvious morphological synapomorphy c. group size d. nomenclatural stability 4. Are ranks arbitrary? a. cladists think so "ranks are simply more or less inclusive" b. not if "gaps" in the pattern of variation are recognized c. if nomenclatural stability is a goal, traditional ranks will tend to be preserved when they are monophyletic
Phylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationReconstructing the history of lineages
Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics
More informationPOPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics
POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the
More informationWhat is Phylogenetics
What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)
More informationInferring phylogeny. Today s topics. Milestones of molecular evolution studies Contributions to molecular evolution
Today s topics Inferring phylogeny Introduction! Distance methods! Parsimony method!"#$%&'(!)* +,-.'/01!23454(6!7!2845*0&4'9#6!:&454(6 ;?@AB=C?DEF Overview of phylogenetic inferences Methodology Methods
More informationLecture V Phylogeny and Systematics Dr. Kopeny
Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437
More informationIntroduction to characters and parsimony analysis
Introduction to characters and parsimony analysis Genetic Relationships Genetic relationships exist between individuals within populations These include ancestordescendent relationships and more indirect
More information8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationC3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
More information--Therefore, congruence among all postulated homologies provides a test of any single character in question [the central epistemological advance].
Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler Jan. 29, 2008. The Hennig Principle: Homology, Synapomorphy, Rooting issues The fundamental
More informationClassification, Phylogeny yand Evolutionary History
Classification, Phylogeny yand Evolutionary History The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize
More informationMolecular Evolution & Phylogenetics
Molecular Evolution & Phylogenetics Heuristics based on tree alterations, maximum likelihood, Bayesian methods, statistical confidence measures Jean-Baka Domelevo Entfellner Learning Objectives know basic
More informationESS 345 Ichthyology. Systematic Ichthyology Part II Not in Book
ESS 345 Ichthyology Systematic Ichthyology Part II Not in Book Thought for today: Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else,
More informationLecture 6 Phylogenetic Inference
Lecture 6 Phylogenetic Inference From Darwin s notebook in 1837 Charles Darwin Willi Hennig From The Origin in 1859 Cladistics Phylogenetic inference Willi Hennig, Cladistics 1. Clade, Monophyletic group,
More information"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley B.D. Mishler Jan. 22, 2009. Trees I. Summary of previous lecture: Hennigian
More informationBIOL 428: Introduction to Systematics Midterm Exam
Midterm exam page 1 BIOL 428: Introduction to Systematics Midterm Exam Please, write your name on each page! The exam is worth 150 points. Verify that you have all 8 pages. Read the questions carefully,
More informationPhylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?
Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them? Carolus Linneaus:Systema Naturae (1735) Swedish botanist &
More informationEvolutionary Tree Analysis. Overview
CSI/BINF 5330 Evolutionary Tree Analysis Young-Rae Cho Associate Professor Department of Computer Science Baylor University Overview Backgrounds Distance-Based Evolutionary Tree Reconstruction Character-Based
More informationSystematics Lecture 3 Characters: Homology, Morphology
Systematics Lecture 3 Characters: Homology, Morphology I. Introduction Nearly all methods of phylogenetic analysis rely on characters as the source of data. A. Character variation is coded into a character-by-taxon
More informationNeed for systematics. Applications of systematics. Linnaeus plus Darwin. Approaches in systematics. Principles of cladistics
Topics Need for systematics Applications of systematics Linnaeus plus Darwin Approaches in systematics Principles of cladistics Systematics pp. 474-475. Systematics - Study of diversity and evolutionary
More informationMany of the slides that I ll use have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!
Many of the slides that I ll use have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Paul has many great tools for teaching phylogenetics at his web site: http://hydrodictyon.eeb.uconn.edu/people/plewis
More informationAnatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses
Anatomy of a tree outgroup: an early branching relative of the interest groups sister taxa: taxa derived from the same recent ancestor polytomy: >2 taxa emerge from a node Anatomy of a tree clade is group
More informationHow should we organize the diversity of animal life?
How should we organize the diversity of animal life? The difference between Taxonomy Linneaus, and Cladistics Darwin What are phylogenies? How do we read them? How do we estimate them? Classification (Taxonomy)
More informationPhylogenetics. BIOL 7711 Computational Bioscience
Consortium for Comparative Genomics! University of Colorado School of Medicine Phylogenetics BIOL 7711 Computational Bioscience Biochemistry and Molecular Genetics Computational Bioscience Program Consortium
More informationPHYLOGENY & THE TREE OF LIFE
PHYLOGENY & THE TREE OF LIFE PREFACE In this powerpoint we learn how biologists distinguish and categorize the millions of species on earth. Early we looked at the process of evolution here we look at
More informationX X (2) X Pr(X = x θ) (3)
Notes for 848 lecture 6: A ML basis for compatibility and parsimony Notation θ Θ (1) Θ is the space of all possible trees (and model parameters) θ is a point in the parameter space = a particular tree
More informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;
More informationCHAPTERS 24-25: Evidence for Evolution and Phylogeny
CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology
More informationEvaluating phylogenetic hypotheses
Evaluating phylogenetic hypotheses Methods for evaluating topologies Topological comparisons: e.g., parametric bootstrapping, constrained searches Methods for evaluating nodes Resampling techniques: bootstrapping,
More informationThanks to Paul Lewis and Joe Felsenstein for the use of slides
Thanks to Paul Lewis and Joe Felsenstein for the use of slides Review Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPGMA infers a tree from a distance
More informationHow to read and make phylogenetic trees Zuzana Starostová
How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation
More informationPhylogenetics: Parsimony
1 Phylogenetics: Parsimony COMP 571 Luay Nakhleh, Rice University he Problem 2 Input: Multiple alignment of a set S of sequences Output: ree leaf-labeled with S Assumptions Characters are mutually independent
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Chapter focus Shifting from the process of how evolution works to the pattern evolution produces over time. Phylogeny Phylon = tribe, geny = genesis or origin
More informationPhylogenetic Inference and Parsimony Analysis
Phylogeny and Parsimony 23 2 Phylogenetic Inference and Parsimony Analysis Llewellyn D. Densmore III 1. Introduction Application of phylogenetic inference methods to comparative endocrinology studies has
More informationBINF6201/8201. Molecular phylogenetic methods
BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics
More informationName. Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014
Name 1 Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014 1. Use the following matrix of nucleotide sequence data and the corresponding tree to answer questions a. through h. below. (16 points)
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence
More informationQuestions we can ask. Recall. Accuracy and Precision. Systematics - Bio 615. Outline
Outline 1. Mechanistic comparison with Parsimony - branch lengths & parameters 2. Performance comparison with Parsimony - Desirable attributes of a method - The Felsenstein and Farris zones - Heterotachous
More informationBiology 211 (2) Week 1 KEY!
Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of
More informationMacroevolution Part I: Phylogenies
Macroevolution Part I: Phylogenies Taxonomy Classification originated with Carolus Linnaeus in the 18 th century. Based on structural (outward and inward) similarities Hierarchal scheme, the largest most
More informationConsensus methods. Strict consensus methods
Consensus methods A consensus tree is a summary of the agreement among a set of fundamental trees There are many consensus methods that differ in: 1. the kind of agreement 2. the level of agreement Consensus
More informationUoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)
- Phylogeny? - Systematics? The Phylogenetic Systematics (Phylogeny and Systematics) - Phylogenetic systematics? Connection between phylogeny and classification. - Phylogenetic systematics informs the
More informationIntegrating Fossils into Phylogenies. Throughout the 20th century, the relationship between paleontology and evolutionary biology has been strained.
IB 200B Principals of Phylogenetic Systematics Spring 2011 Integrating Fossils into Phylogenies Throughout the 20th century, the relationship between paleontology and evolutionary biology has been strained.
More informationClassification and Phylogeny
Classification and Phylogeny The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
More informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley. Parsimony & Likelihood [draft]
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley K.W. Will Parsimony & Likelihood [draft] 1. Hennig and Parsimony: Hennig was not concerned with parsimony
More informationClassification and Phylogeny
Classification and Phylogeny The diversity it of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
More informationPhylogenetic methods in molecular systematics
Phylogenetic methods in molecular systematics Niklas Wahlberg Stockholm University Acknowledgement Many of the slides in this lecture series modified from slides by others www.dbbm.fiocruz.br/james/lectures.html
More informationParsimony via Consensus
Syst. Biol. 57(2):251 256, 2008 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150802040597 Parsimony via Consensus TREVOR C. BRUEN 1 AND DAVID
More informationFinding the best tree by heuristic search
Chapter 4 Finding the best tree by heuristic search If we cannot find the best trees by examining all possible trees, we could imagine searching in the space of possible trees. In this chapter we will
More informationMolecular Phylogenetics and Evolution
Molecular Phylogenetics and Evolution 61 (2011) 177 191 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Spurious 99% bootstrap
More informationAP Biology. Cladistics
Cladistics Kingdom Summary Review slide Review slide Classification Old 5 Kingdom system Eukaryote Monera, Protists, Plants, Fungi, Animals New 3 Domain system reflects a greater understanding of evolution
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationLaboratory IV Phylogenetic Reconstruction
Laboratory IV Phylogenetic Reconstruction Objective: In this week s lab you will learn how to reconstruct evolutionary relationships. Biologists have experimented with a variety of methods for interpreting
More informationNomenclature and classification
Class entry quiz results year biology background major biology freshman college advanced environmental sophomore sciences college introductory landscape architecture junior highschool undeclared senior
More informationBiologists have used many approaches to estimating the evolutionary history of organisms and using that history to construct classifications.
Phylogenetic Inference Biologists have used many approaches to estimating the evolutionary history of organisms and using that history to construct classifications. Willi Hennig developed d the techniques
More informationPhylogeny 9/8/2014. Evolutionary Relationships. Data Supporting Phylogeny. Chapter 26
Phylogeny Chapter 26 Taxonomy Taxonomy: ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Carolus Linnaeus developed binomial nomenclature,
More informationMichael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D
7.91 Lecture #5 Database Searching & Molecular Phylogenetics Michael Yaffe B C D B C D (((,B)C)D) Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood
More informationIs the equal branch length model a parsimony model?
Table 1: n approximation of the probability of data patterns on the tree shown in figure?? made by dropping terms that do not have the minimal exponent for p. Terms that were dropped are shown in red;
More informationEstimating Phylogenies (Evolutionary Trees) II. Biol4230 Thurs, March 2, 2017 Bill Pearson Jordan 6-057
Estimating Phylogenies (Evolutionary Trees) II Biol4230 Thurs, March 2, 2017 Bill Pearson wrp@virginia.edu 4-2818 Jordan 6-057 Tree estimation strategies: Parsimony?no model, simply count minimum number
More informationPhylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationPhylogeny. Properties of Trees. Properties of Trees. Trees represent the order of branching only. Phylogeny: Taxon: a unit of classification
Multiple sequence alignment global local Evolutionary tree reconstruction Pairwise sequence alignment (global and local) Substitution matrices Gene Finding Protein structure prediction N structure prediction
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationFig. 26.7a. Biodiversity. 1. Course Outline Outcomes Instructors Text Grading. 2. Course Syllabus. Fig. 26.7b Table
Fig. 26.7a Biodiversity 1. Course Outline Outcomes Instructors Text Grading 2. Course Syllabus Fig. 26.7b Table 26.2-1 1 Table 26.2-2 Outline: Systematics and the Phylogenetic Revolution I. Naming and
More informationMolecular Evolution and Phylogenetics...a very short course
and Phylogenetics...a very short course Hernán J. Dopazo Pharmacogenomics and Comparative Genomics Unit Bioinformatics Department Centro de Investigación Príncipe Felipe CIPF Valencia - Spain 2005 Page
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationThe Tree of Life. Phylogeny
The Tree of Life Phylogeny Phylogenetics Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein sequences Each branch
More informationTree of Life iological Sequence nalysis Chapter http://tolweb.org/tree/ Phylogenetic Prediction ll organisms on Earth have a common ancestor. ll species are related. The relationship is called a phylogeny
More informationThe practice of naming and classifying organisms is called taxonomy.
Chapter 18 Key Idea: Biologists use taxonomic systems to organize their knowledge of organisms. These systems attempt to provide consistent ways to name and categorize organisms. The practice of naming
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationPhylogenetic Trees. Phylogenetic Trees Five. Phylogeny: Inference Tool. Phylogeny Terminology. Picture of Last Quagga. Importance of Phylogeny 5.
Five Sami Khuri Department of Computer Science San José State University San José, California, USA sami.khuri@sjsu.edu v Distance Methods v Character Methods v Molecular Clock v UPGMA v Maximum Parsimony
More informationPatterns of Evolution
Patterns of Evolution A tree that represents an estimate (hypothesis) of evolutionary relatedness is a phylogeny Classifications can be based on groupings within a phylogeny Groupings can be categorized
More informationBiology 1B Evolution Lecture 2 (February 26, 2010) Natural Selection, Phylogenies
1 Natural Selection (Darwin-Wallace): There are three conditions for natural selection: 1. Variation: Individuals within a population have different characteristics/traits (or phenotypes). 2. Inheritance:
More informationPhylogeny. November 7, 2017
Phylogeny November 7, 2017 Phylogenetics Phylon = tribe/race, genetikos = relative to birth Phylogenetics: study of evolutionary relationships among organisms, sequences, or anything in between Related
More informationClassifications can be based on groupings g within a phylogeny
Patterns of Evolution A tree that represents an estimate (hypothesis) of evolutionary relatedness is a phylogeny Classifications can be based on groupings g within a phylogeny y Groupings can be categorized
More informationChapter 10. Classification and Phylogeny of Animals. Order in Diversity. Hierarchy of taxa. Table Linnaeus introduced binomial nomenclature
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chapter 10 Classification and Phylogeny of Animals Order in Diversity History Systematic zoologists have three
More information1/27/2010. Systematics and Phylogenetics of the. An Introduction. Taxonomy and Systematics
Systematics and Phylogenetics of the Amphibia: An Introduction Taxonomy and Systematics Taxonomy, the science of describing biodiversity, mainly naming unnamed species, and arranging the diversity into
More informationA (short) introduction to phylogenetics
A (short) introduction to phylogenetics Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR Statistics, Millport Field
More informationPhylogenetics: Parsimony and Likelihood. COMP Spring 2016 Luay Nakhleh, Rice University
Phylogenetics: Parsimony and Likelihood COMP 571 - Spring 2016 Luay Nakhleh, Rice University The Problem Input: Multiple alignment of a set S of sequences Output: Tree T leaf-labeled with S Assumptions
More informationPhylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline
Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying
More informationBootstrap confidence levels for phylogenetic trees B. Efron, E. Halloran, and S. Holmes, 1996
Bootstrap confidence levels for phylogenetic trees B. Efron, E. Halloran, and S. Holmes, 1996 Following Confidence limits on phylogenies: an approach using the bootstrap, J. Felsenstein, 1985 1 I. Short
More informationBioinformatics 1. Sepp Hochreiter. Biology, Sequences, Phylogenetics Part 4. Bioinformatics 1: Biology, Sequences, Phylogenetics
Bioinformatics 1 Biology, Sequences, Phylogenetics Part 4 Sepp Hochreiter Klausur Mo. 30.01.2011 Zeit: 15:30 17:00 Raum: HS14 Anmeldung Kusss Contents Methods and Bootstrapping of Maximum Methods Methods
More informationSystematics - Bio 615
Bayesian Phylogenetic Inference 1. Introduction, history 2. Advantages over ML 3. Bayes Rule 4. The Priors 5. Marginal vs Joint estimation 6. MCMC Derek S. Sikes University of Alaska 7. Posteriors vs Bootstrap
More informationHistorical Biogeography. Historical Biogeography. Systematics
Historical Biogeography I. Definitions II. Fossils: problems with fossil record why fossils are important III. Phylogeny IV. Phenetics VI. Phylogenetic Classification Disjunctions debunked: Examples VII.
More information"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2011 University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2011 University of California, Berkeley B.D. Mishler March 31, 2011. Reticulation,"Phylogeography," and Population Biology:
More informationPhylogenetic analyses. Kirsi Kostamo
Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,
More informationPhylogenetic Tree Reconstruction
I519 Introduction to Bioinformatics, 2011 Phylogenetic Tree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Evolution theory Speciation Evolution of new organisms is driven
More informationAlgorithms in Bioinformatics
Algorithms in Bioinformatics Sami Khuri Department of Computer Science San José State University San José, California, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri Distance Methods Character Methods
More informationPhylogeny and the Tree of Life
LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 26 Phylogeny and the Tree of Life
More informationPhylogenetic Analysis. Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center
Phylogenetic Analysis Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center Outline Basic Concepts Tree Construction Methods Distance-based methods
More informationLecture 11 Friday, October 21, 2011
Lecture 11 Friday, October 21, 2011 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system
More informationEstimating Evolutionary Trees. Phylogenetic Methods
Estimating Evolutionary Trees v if the data are consistent with infinite sites then all methods should yield the same tree v it gets more complicated when there is homoplasy, i.e., parallel or convergent
More informationPrinciples of Phylogeny Reconstruction How do we reconstruct the tree of life? Basic Terminology. Looking at Trees. Basic Terminology.
Principles of Phylogeny Reconstruction How do we reconstruct the tree of life? Phylogeny: asic erminology Outline: erminology Phylogenetic tree: Methods Problems parsimony maximum likelihood bootstrapping
More informationCHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny
CHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny To trace phylogeny or the evolutionary history of life, biologists use evidence from paleontology, molecular data, comparative
More informationChapter 19: Taxonomy, Systematics, and Phylogeny
Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand
More informationPhylogeny: building the tree of life
Phylogeny: building the tree of life Dr. Fayyaz ul Amir Afsar Minhas Department of Computer and Information Sciences Pakistan Institute of Engineering & Applied Sciences PO Nilore, Islamabad, Pakistan
More informationA Chain Is No Stronger than Its Weakest Link: Double Decay Analysis of Phylogenetic Hypotheses
Syst. Biol. 49(4):754 776, 2000 A Chain Is No Stronger than Its Weakest Link: Double Decay Analysis of Phylogenetic Hypotheses MARK WILKINSON, 1 JOSEPH L. THORLEY, 1,2 AND PAUL UPCHURCH 3 1 Department
More informationPHYLOGENY AND SYSTEMATICS
AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study
More information