Inferring Molecular Phylogeny
|
|
- Sophie Matthews
- 5 years ago
- Views:
Transcription
1 r. Walter Salzburger The tree of life, ustav Klimt (1907) Inferring Molecular Phylogeny Inferring Molecular Phylogeny 2 1. Molecular Markers
2 Inferring Molecular Phylogeny 3 Immunological comparisons! Nuttall & Uhlenhuth (early 20th century): blood relationships between species! cross reaction between sera and anti-sera! strategy: the degree of similarity reflects the strength of the evolutionary relationships Inferring Molecular Phylogeny 4 vise (1994)
3 Inferring Molecular Phylogeny 5 Protein electrophoresis! developed by Hunter & Markert (1957)! non-denatured proteins with different net charges migrate at different rates through starch or acrylamide gels! histochemical stains specific for enzymes under assay! zymograms are interpretable in terms of Mendelian genotypes Inferring Molecular Phylogeny 6
4 Inferring Molecular Phylogeny 7 vise (1994) Inferring Molecular Phylogeny 8 Restriction endonucleases! Linn & rber*, Meselson & Yuan (1968): discovery of restriction endonucleases (enzymes) i.e., precise scalpels to cut double-stranded N at specific motifs *Nobel Prize in Physiology or Medicine 1978
5 Inferring Molecular Phylogeny 9 Inferring Molecular Phylogeny 10 Recombinant N technology
6 Inferring Molecular Phylogeny 11 Restriction digestion! restriction digestion profiles! phylogenetic, population genetic markers! presence/absence matrix! used for: mitochondria, plastids, whole genomes, after PR amplification, etc. Inferring Molecular Phylogeny 12 Restriction fragment length polymorphism
7 Inferring Molecular Phylogeny 13 Inferring Molecular Phylogeny 14 mplified fragment length polymorphism
8 Inferring Molecular Phylogeny 15 N-N hybridization!...relies on the double-stranded nature of N!...and that complementary strands are held together by hydrogen bonds! when N is heated, it melts into single strands, if it is cooled, it re-associates! data: thermal elusion profiles Inferring Molecular Phylogeny 16 vise (1994)
9 Inferring Molecular Phylogeny 17 issociation curves! homoduplex hybridization (intraspecific)! heteroduplex hybridization (interspecific)! genetic distance ~ "Thomo - "Thetero heteroduplex ostrich-rhea vise (1994) homoduplex ostrich Inferring Molecular Phylogeny 18 Sibley & hlquist (1980s) Sibley & hlquist (1990)
10 Inferring Molecular Phylogeny 19 N Sequencing! Walter ilbert and Fred Sanger develop techniques for N sequencing (1977) Walter ilbert (1932-) Fred Sanger (1918-) Nobel Prize in hemistry 1980 Inferring Molecular Phylogeny 20 Polymerase hain Reaction (PR)! In the 1980s, Kary. Mullis invents and helps to develop further the PR Kary. Mullis (1944-) Nobel Prize in hemistry 1993
11 Inferring Molecular Phylogeny Inferring Phylogenies ocuments of volutionary History 22 space...ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......ttt......tttt......tttt......tttt......tttt......tttt......tttt... time...tt......tt......tt......tt......tttt......tttt......tttt......tttt......tttt......tttt......tttt......tttt...
12 ocuments of volutionary History 23...TTT......TT......TTT......TTTT......TTTT......TTTT... time Inferring Molecular Phylogeny 24 TTT TTT TTTT TTTT raw N sequences alignment* TTT TTT TTT--T TTT--T gap aligned N sequences *lignment: inferring homology at the N sequence level
13 Inferring Molecular Phylogeny 25 TTT TTT phylogeny reconstruction TTT--T TTT--T molecular phylogeny aligned N sequences Inferring Molecular Phylogeny Sequence lignment
14 Inferring Molecular Phylogeny 27 Homology!...similarity between characters due to shared ancestry! Two nucleotides in different sequences are homologous if (and only if) the sequences both acquired that state from their common ancestor homologous character homoplasious character Inferring Molecular Phylogeny 28 lignment!...set of homologous sequences in which every nucleotide position is homologous! to align : inferring homology at the sequence level HO1! 1! K1! R1!! TTTT! TTTT! TTTT! TTTT HO1! 1! K1! R1!! TTTT! TTTT! TT-TT! TT-TT gap
15 Inferring Molecular Phylogeny 29 Pairwise alignment I: gaps Sequence1 TTTT Sequence2 TTT 1 Sequence1 TTTT Sequence2! TTT 2 Sequence1 T---TTT Sequence2 TTT 2 1 T!!!!!!!!! T!!!!!!!!!!!! T!!!!! T T T T dot plot Inferring Molecular Phylogeny 30 Pairwise alignment II: sequences that differ Sequence1 TTT Sequence2 TTT 1 Sequence1 TTT Sequence2! TTT 1 T!!!!!! T!!!!!!!!!! T!!!! T T T
16 Inferring Molecular Phylogeny 31 Pairwise alignment III: the cost of an alignment number of substitutions cost = s + wg total length of gaps gap penalty w = 1 : gap is as expensive as a substitution w = 2 : gap is twice as expensive as a substitution Inferring Molecular Phylogeny 32 Pairwise alignment IV: evaluating alternatives Sequence1 TTTT Sequence2 TT 1 Sequence1 TTTT Sequence2 T-T 2 Sequence1 T--TTT Sequence2! TT 2 1!! T!!!!!!!!!!!!!!!! T!!!!! T T T T dot plot
17 Inferring Molecular Phylogeny 33 Pairwise alignment IV: evaluating alternatives Sequence1 TTTT Sequence2 TT = s + wg 1 Sequence1 TTTT Sequence2 T-T 2 Sequence1 T--TTT Sequence2! TT (w=1) = x 1 = 3 (w=3) = x 1 = 5 (w=1) = x 2 = 2 (w=3) = x 2 = 6 Inferring Molecular Phylogeny 34 LST: asic Local lignment Search Tool! regions of local similarity between nucleotide or protein sequences and calculates the statistical significance of matches!...uses databases in enank*!...see official NI handbook, chapter 16 (on course web page) *nucleotide and protein database of the National enter for iotechnolgy Information
18 Inferring Molecular Phylogeny 35 Multiple alignment! sum-of-pairs: minimizing the costs of all pairwise alignments (e.g., computer program lustalw)! tree alignment: uses phylogenetic information! star alignment: all sequences are equally related! tree alignment: phylogenetic relationships between sequences are taken into account Inferring Molecular Phylogeny 36 Protein alignments: PM and LOSUM matrices S T P N Q H R K M I L V F Y W 9 ysteine S -1 4 T P Hydrophilic N cid amide Q H R asic K M I Hydro- L phobic V F Y romatic M LOSUM62 PM... Position ccepted Mutation LOSUM... Locks SUbstitution Matrix
19 Inferring Molecular Phylogeny Phylogenetic Methods! istance Methods! UPM! Neighbor joining! Minimum volution " Maximum Parsimony " Maximum Likelihood " ML! ayesian Inference genetic distance Seq Seq Seq Seq Seq Seq nucleotide sequence Seq T T T T Seq T T T Seq T Seq T Inferring Molecular Phylogeny 38 iscrete character vs. distance method genetic distance Seq Seq Seq Seq Seq Seq T> T> T>T> T> >T 7 >T nucleotide sequence Seq T T T T Seq T T T Seq T Seq T
20 luster methods: step-by-step approach starting tree 1 add next sequence Round 1 Round 2 starting tree 2 place next sequence add next sequence? place next sequence? Inferring Molecular Phylogeny 39 Optimally criterion: choose among all possible trees Inferring Molecular Phylogeny 40
21 Inferring Molecular Phylogeny 41 Optimally criterion: too many trees problem... number of taxa number of trees (unrooted) number of trees (rooted) Inferring Molecular Phylogeny 42 Type of data istances Nucleotides Tree building method lustering algorithm Optimally criterion UPM Neighbor joining Minimum volution Maximum Parsimony Maximum Likelihood
22 Inferring Molecular Phylogeny 43 UPM: unpaired group method with arithmetic means distance matrix Sequence TTT Sequence TT haracter Taxon Taxon pigment 1 0 fins 1 1 eyes 1 1 teeth 0 1 Inferring Molecular Phylogeny 44 UPM: unpaired group method with arithmetic means 1 distance matrix ultrametric tree
23 Inferring Molecular Phylogeny 45 Neighbor joining (NJ) 5 1 distance matrix additive tree Inferring Molecular Phylogeny 46 Minimum evolution (M) total number of branches in a tree of n sequences 2n-3 tree length L =!ei i=1 individual branch length! The minimum evolution tree is the one that minimizes L
24 Inferring Molecular Phylogeny 47 Minimum evolution (M): example Human himp orilla Orang-utan ibbon Human himp orilla Orang-utan ibbon pairwise distances between hominoid sequences observed calculated Inferring Molecular Phylogeny 48 Minimum evolution (M): example ibbon Orang-utan orilla Human himpanzee
25 Inferring Molecular Phylogeny 49 Maximum Parsimony (MP)! Maximum parsimony principle: preference for the least complex explanation for an observation! in phylogenetics: choosing the tree that requires the fewest evolutionary changes ( most parsimonious tree )...! i.e., the tree that requires the fewest mutational steps...! i.e., the tree with the shortest tree length Inferring Molecular Phylogeny 50 Maximum Parsimony (MP) number of nucleotide sites k tree length L =!li i=1 tree length for an individual site! The most parsimonious tree is the one that minimizes L
26 Inferring Molecular Phylogeny 51 Maximum Parsimony (MP) alignment Site Taxon T T T Taxon T T Taxon T Taxon T Inferring Molecular Phylogeny 52 Maximum Parsimony (MP) alignment Site Taxon T T T Taxon T T Taxon T Taxon T Site 1 change 1 change 2 changes 2 changes
27 Inferring Molecular Phylogeny 53 Maximum Parsimony (MP) alignment Site Taxon T T T Taxon T T Taxon T Taxon T Site 1 1 change T T Site 2 1 change Site 3 Site 4 T Site 5 T 1 change T 1 change T 0 change T Inferring Molecular Phylogeny 54 Maximum Parsimony (MP) Sites Tree Total ((,),(,)) ((,),(,)) ((,),(,))
Theory of Evolution. Charles Darwin
Theory of Evolution harles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (8-6) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties
More informationTheory of Evolution Charles Darwin
Theory of Evolution Charles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (83-36) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties
More informationTHEORY. Based on sequence Length According to the length of sequence being compared it is of following two types
Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between
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 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 informationPage 1. Evolutionary Trees. Why build evolutionary tree? Outline
Page Evolutionary Trees Russ. ltman MI S 7 Outline. Why build evolutionary trees?. istance-based vs. character-based methods. istance-based: Ultrametric Trees dditive Trees. haracter-based: Perfect phylogeny
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 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 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 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 informationBioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony
ioinformatics -- lecture 9 Phylogenetic trees istance-based tree building Parsimony (,(,(,))) rees can be represented in "parenthesis notation". Each set of parentheses represents a branch-point (bifurcation),
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
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 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 informationPhylogenetic inference
Phylogenetic inference Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, March 7 th 016 After this lecture, you can discuss (dis-) advantages of different information types
More informationPhylogenetics: Building Phylogenetic Trees
1 Phylogenetics: Building Phylogenetic Trees COMP 571 Luay Nakhleh, Rice University 2 Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary model should
More informationPhylogenetics: Building Phylogenetic Trees. COMP Fall 2010 Luay Nakhleh, Rice University
Phylogenetics: Building Phylogenetic Trees COMP 571 - Fall 2010 Luay Nakhleh, Rice University Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary
More informationPhylogeny Tree Algorithms
Phylogeny Tree lgorithms Jianlin heng, PhD School of Electrical Engineering and omputer Science University of entral Florida 2006 Free for academic use. opyright @ Jianlin heng & original sources for some
More informationPhylogenetic inference: from sequences to trees
W ESTFÄLISCHE W ESTFÄLISCHE W ILHELMS -U NIVERSITÄT NIVERSITÄT WILHELMS-U ÜNSTER MM ÜNSTER VOLUTIONARY FUNCTIONAL UNCTIONAL GENOMICS ENOMICS EVOLUTIONARY Bioinformatics 1 Phylogenetic inference: from sequences
More informationThe use of molecular tools for taxonomic research in zoology & botany
The use of molecular tools for taxonomic research in zoology & botany Outline Why employ molecular genetic markers? Brief historical overview of DN research Molecular techniques for genetic analysis DN
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 informationThanks to Paul Lewis, Jeff Thorne, and Joe Felsenstein for the use of slides
hanks to Paul Lewis, Jeff horne, and Joe Felsenstein for the use of slides Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPM infers a tree from a distance
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 informationPhylogenetic Trees. What They Are Why We Do It & How To Do It. Presented by Amy Harris Dr Brad Morantz
Phylogenetic Trees What They Are Why We Do It & How To Do It Presented by Amy Harris Dr Brad Morantz Overview What is a phylogenetic tree Why do we do it How do we do it Methods and programs Parallels
More informationIntraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation
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 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 information9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)
I9 Introduction to Bioinformatics, 0 Phylogenetic ree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & omputing, IUB Evolution theory Speciation Evolution of new organisms is driven by
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 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 informationMolecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016
Molecular phylogeny - Using molecular sequences to infer evolutionary relationships Tore Samuelsson Feb 2016 Molecular phylogeny is being used in the identification and characterization of new pathogens,
More information08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega
BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments
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 informationEVOLUTIONARY DISTANCES
EVOLUTIONARY DISTANCES FROM STRINGS TO TREES Luca Bortolussi 1 1 Dipartimento di Matematica ed Informatica Università degli studi di Trieste luca@dmi.units.it Trieste, 14 th November 2007 OUTLINE 1 STRINGS:
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 informationBioinformatics tools for phylogeny and visualization. Yanbin Yin
Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and
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 informationInferring Molecular Phylogeny
Dr. Walter Salzburger he tree of life, ustav Klimt (1907) Inferring Molecular Phylogeny Inferring Molecular Phylogeny 55 Maximum Parsimony (MP): objections long branches I!! B D long branch attraction
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 informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
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 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 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 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 informationPhylogenetics: Distance Methods. COMP Spring 2015 Luay Nakhleh, Rice University
Phylogenetics: Distance Methods COMP 571 - Spring 2015 Luay Nakhleh, Rice University Outline Evolutionary models and distance corrections Distance-based methods Evolutionary Models and Distance Correction
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 informationDNA Phylogeny. Signals and Systems in Biology Kushal EE, IIT Delhi
DNA Phylogeny Signals and Systems in Biology Kushal Shah @ EE, IIT Delhi Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics :
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 informationAlgorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment
Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot
More informationSeuqence Analysis '17--lecture 10. Trees types of trees Newick notation UPGMA Fitch Margoliash Distance vs Parsimony
Seuqence nalysis '17--lecture 10 Trees types of trees Newick notation UPGM Fitch Margoliash istance vs Parsimony Phyogenetic trees What is a phylogenetic tree? model of evolutionary relationships -- common
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 informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
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 informationA Phylogenetic Network Construction due to Constrained Recombination
A Phylogenetic Network Construction due to Constrained Recombination Mohd. Abdul Hai Zahid Research Scholar Research Supervisors: Dr. R.C. Joshi Dr. Ankush Mittal Department of Electronics and Computer
More informationInferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT
Inferring phylogeny Constructing phylogenetic trees Tõnu Margus Contents What is phylogeny? How/why it is possible to infer it? Representing evolutionary relationships on trees What type questions questions
More informationTaxonomy. Content. How to determine & classify a species. Phylogeny and evolution
Taxonomy Content Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Phylogeny and evolution Why Taxonomy? Classification Arrangement in groups or taxa (taxon = group) Nomenclature
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 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 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 informationMolecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço
Molecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço jcarrico@fm.ul.pt Charles Darwin (1809-1882) Charles Darwin s tree of life in Notebook B, 1837-1838 Ernst Haeckel (1934-1919)
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 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 Todd Vision Spring Some applications. Uncultured microbial diversity
Phylogenetics Todd Vision Spring 2008 Tree basics Sequence alignment Inferring a phylogeny Neighbor joining Maximum parsimony Maximum likelihood Rooting trees and measuring confidence Software and file
More informationGel Electrophoresis. 10/28/0310/21/2003 CAP/CGS 5991 Lecture 10Lecture 9 1
Gel Electrophoresis Used to measure the lengths of DNA fragments. When voltage is applied to DNA, different size fragments migrate to different distances (smaller ones travel farther). 10/28/0310/21/2003
More informationC.DARWIN ( )
C.DARWIN (1809-1882) LAMARCK Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation DARWIN All organisms are historically interconnected. Their relationships
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 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 informationIntroduction to Bioinformatics Introduction to Bioinformatics
Dr. rer. nat. Gong Jing Cancer Research Center Medicine School of Shandong University 2012.11.09 1 Chapter 4 Phylogenetic Tree 2 Phylogeny Evidence from morphological ( 形态学的 ), biochemical, and gene sequence
More informationPhylogenetics in the Age of Genomics: Prospects and Challenges
Phylogenetics in the Age of Genomics: Prospects and Challenges Antonis Rokas Department of Biological Sciences, Vanderbilt University http://as.vanderbilt.edu/rokaslab http://pubmed2wordle.appspot.com/
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 informationCurriculum Links. AQA GCE Biology. AS level
Curriculum Links AQA GCE Biology Unit 2 BIOL2 The variety of living organisms 3.2.1 Living organisms vary and this variation is influenced by genetic and environmental factors Causes of variation 3.2.2
More informationMultiple Sequence Alignment, Gunnar Klau, December 9, 2005, 17:
Multiple Sequence Alignment, Gunnar Klau, December 9, 2005, 17:50 5001 5 Multiple Sequence Alignment The first part of this exposition is based on the following sources, which are recommended reading:
More informationMolecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
More informationMolecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
More informationSequence Analysis 17: lecture 5. Substitution matrices Multiple sequence alignment
Sequence Analysis 17: lecture 5 Substitution matrices Multiple sequence alignment Substitution matrices Used to score aligned positions, usually of amino acids. Expressed as the log-likelihood ratio of
More informationBIOINFORMATICS: An Introduction
BIOINFORMATICS: An Introduction What is Bioinformatics? The term was first coined in 1988 by Dr. Hwa Lim The original definition was : a collective term for data compilation, organisation, analysis and
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 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 informationa,bD (modules 1 and 10 are required)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the
More informationCopyright notice. Molecular Phylogeny and Evolution. Goals of the lecture. Introduction. Introduction. December 15, 2008
opyright notice Molecular Phylogeny and volution ecember 5, 008 ioinformatics J. Pevsner pevsner@kennedykrieger.org Many of the images in this powerpoint presentation are from ioinformatics and Functional
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 informationFirst generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences
First generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences 140.638 where do sequences come from? DNA is not hard to extract (getting DNA from a
More informationHomework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics:
Homework Assignment, Evolutionary Systems Biology, Spring 2009. Homework Part I: Phylogenetics: Introduction. The objective of this assignment is to understand the basics of phylogenetic relationships
More informationTools and Algorithms in Bioinformatics
Tools and Algorithms in Bioinformatics GCBA815, Fall 2015 Week-4 BLAST Algorithm Continued Multiple Sequence Alignment Babu Guda, Ph.D. Department of Genetics, Cell Biology & Anatomy Bioinformatics and
More informationMultiple Sequence Alignment
Multiple equence lignment Four ami Khuri Dept of omputer cience an José tate University Multiple equence lignment v Progressive lignment v Guide Tree v lustalw v Toffee v Muscle v MFFT * 20 * 0 * 60 *
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 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 informationMolecular evolution. Joe Felsenstein. GENOME 453, Autumn Molecular evolution p.1/49
Molecular evolution Joe Felsenstein GENOME 453, utumn 2009 Molecular evolution p.1/49 data example for phylogeny inference Five DN sequences, for some gene in an imaginary group of species whose names
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 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 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 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 informationChapter 16: Reconstructing and Using Phylogenies
Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/
More informationCS5263 Bioinformatics. Guest Lecture Part II Phylogenetics
CS5263 Bioinformatics Guest Lecture Part II Phylogenetics Up to now we have focused on finding similarities, now we start focusing on differences (dissimilarities leading to distance measures). Identifying
More informationBootstraps and testing trees. Alog-likelihoodcurveanditsconfidenceinterval
ootstraps and testing trees Joe elsenstein epts. of Genome Sciences and of iology, University of Washington ootstraps and testing trees p.1/20 log-likelihoodcurveanditsconfidenceinterval 2620 2625 ln L
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 informationSequencing alignment Ameer Effat M. Elfarash
Sequencing alignment Ameer Effat M. Elfarash Dept. of Genetics Fac. of Agriculture, Assiut Univ. amir_effat@yahoo.com Why perform a multiple sequence alignment? MSAs are at the heart of comparative genomics
More informationConsistency Index (CI)
Consistency Index (CI) minimum number of changes divided by the number required on the tree. CI=1 if there is no homoplasy negatively correlated with the number of species sampled Retention Index (RI)
More informationMolecular Evolution, course # Final Exam, May 3, 2006
Molecular Evolution, course #27615 Final Exam, May 3, 2006 This exam includes a total of 12 problems on 7 pages (including this cover page). The maximum number of points obtainable is 150, and at least
More information