Molecular evolution 2. Please sit in row K or forward
|
|
- Caitlin Miles
- 5 years ago
- Views:
Transcription
1 Molecular evolution 2 Please sit in row K or forward
2 RBFD: cat, mouse, parasite Toxoplamsa gondii cyst in a mouse brain Credit: Jitinder P. Dubey
3 Topics for the next few days The HIV genome in context Phylogenetic trees of hosts vs. pathogens: introducing the HIV/SIV case Phylogenetic reconstruction methods Constructing a distance matrix between sequences What is a sequence alignment? The Jukes-Cantor correction The neighbor-joining algorithm to make a tree from distances
4 The HIV genome in context Human E. coli Mimivirus M. genitalium HIV LINE transposon SINE transposon ~20,000 ~4000 ~1000 ~ Variation in protein coding gene count
5 HIV (entire genome) E. coli (~25 thousand bp on the E. coli chromosome) Human (~1 million bp on human chromosome 4)
6 Topics for the next few days The HIV genome in context Phylogenetic trees of hosts vs. pathogens: introducing the HIV/SIV case Phylogenetic reconstruction methods Constructing a distance matrix between sequences What is a sequence alignment? The Jukes-Cantor correction The neighbor-joining algorithm to make a tree from distances
7 HIV and SIV
8 Question: If we made a tree for the HIV/SIV sequences infecting these primates, how would it compare with this host tree? Gabon talapoin Sooty mangabey Drill Chimp Human Phylogeny from Perelman et al. molecular phylogeny of living primates 2011.
9 The data Strain and host HIV1_human_a HIV1_human_b HIV1_human_c HIV1_human_d HIV1_human_e SIV_chimp_a SIV_chimp_b HIV2_human_a HIV2_human_b HIV2_human_c SIV_sootyMangabey_a SIV_sootyMangabey_b SIV_drill SIV_gabonTalapoin HTLV-1 Sequence TTTTTTGGGTTTGGC... TTTTTTGGGGTTTGGC... TTTTTTGGCTCTGGC... TTTTTTGGGGGCTGGT... TTTTTTGGGGTCTGGC... TTTTTTGGGCGCCCC... TTTTTTGGGGGGCTGGC... TTTTTTGGGTGGGCTCC... TTTTTTGGGTTGGCCCT... TTTTTTGGGTTTGGCCCT... TTTTTTGGTTTGGCCCT... TTTTTTGGTTTGGTCCTT... TTTTTTGGGTCTCCCT... TTTTTTGGGGTCTTTTT... TGCGCTGGCCCTTCCT...
10 Representing nucleic acid molecules on a computer UUUUUUGGGGUCUGGCCUUCCUCGGG By convention, we represent as a single string going 5' to 3.
11 Representing nucleic acid molecules on a computer 5' TTTTTTGGGGTCTGGCCTTCCTCGGG 3' 3' TCCCTTCTGCCGGGGTGTTCCCTT 5' TTTTTTGGGGTCTGGCCTTCCTCGGG or Either of these ok Called reverse complements TTCCCTTGTGGGGCCGTCTTCCCT
12 Topics for the next few days The HIV genome in context Phylogenetic trees of hosts vs. pathogens: introducing the HIV/SIV case Phylogenetic reconstruction methods Constructing a distance matrix between sequences What is a sequence alignment? The Jukes-Cantor correction The neighbor-joining algorithm to make a tree from distances
13 Trees and distances: often substitutions accumulate (roughly) proportional to time B C D time
14 What is a sequence alignment? GTCGGT GTCGGT GTCCGCT GTCCGCT Our goal: to obtain distances between sequences by estimating the number of substitutions
15 What is a sequence alignment? GTCGGT GTCGGT GTCCGCT lignment process GTCCGCT G-T--CGGT GTCCGCT
16 Topics for the next few days The HIV genome in context Phylogenetic trees of hosts vs. pathogens: introducing the HIV/SIV case Phylogenetic reconstruction methods Constructing a distance matrix between sequences What is a sequence alignment? The Jukes-Cantor correction The neighbor-joining algorithm to make a tree from distances
17 Distances from alignments: estimating the number of substitutions Partial alignment from the gag gene: SIV_deBrazzaMonkey: TTTCTGGGTT HIV2_human_a: TGT------GCGGT Ignore sites with a gap character. How many substitutions occurred between these two sequences since their last common ancestor? Number of sequence differences at non-gap sites: 6 Does this mean there were 6 substitutions?
18 Number of substitutions vs. number of observed differences C T G T T G C G T T G G G T T T G T
19 Number of substitutions vs. number of observed differences T T G T TT GT Number of observed differences (3) is less than true number of substitutions (5).
20 Correcting for multiple hits with the probabilistic Jukes-Cantor model C Model a single nucleotide position G T Series of discrete time steps
21 Correcting for multiple hits with the probabilistic Jukes-Cantor model Model a single nucleotide position P (0) = 1 P (1) = G C T Series of discrete time steps
22 Correcting for multiple hits with the probabilistic Jukes-Cantor model Model a single nucleotide position P (0) = 1 P (1) = 1 3a G C T Series of discrete time steps
23 Two ways we can have nucleotide n at time t+1: 1. Nucleotide present: Time: n n t t+1 stays same 2. Nucleotide present: Time: not n n t t+1 changes to n Write an expression for P n (t+1) in terms of P n (t) and : P n (t +1) =
24 Two ways we can have nucleotide n at time t+1: 1. Nucleotide present: Time: n n t t+1 stays same 2. Nucleotide present: Time: not n n t t+1 changes to n Write an expression for P n (t+1) in terms of P n (t) and : P n (t +1) = (1 3)P n (t)+ [ 1 P n (t)]
25 Expression for the change in probability of nucleotide n, arising over one time step, from time t to time t+1.
26 Expression for the change in probability of nucleotide n, arising over one time step, from time t to time t+1. ΔP n (t) = P n (t +1) P n (t) ΔP n (t) = P n (t) 3P n (t)+ P n (t) P n (t) ΔP n (t) = 4P n (t)+
27 P n (0) P n (t) dp n (t) dt Math 45 = 4P n (t)+ P n (t) = " P (0) 1 % $ n # 4 & 'e 4t Probability of j at time t given j at time 0.! "" # = )*+,- Probability of k at time t given j at time 0.! ". # = )*+,-
28 Worksheet (Rip it off from the back of your packet) Name:! "" # = )*+,-! ". # = )*+,- 1. If the nucleotide is C at time 0, ie P C (0)=1, what is the probability is is C after a long time? 2. If the nucleotide is C at time 0, ie P C (0)=1, what is the probability it is G after a long time? 3. What are the equilibrium nucleotide frequencies we would expect as a result of this process? In other words, if we had a long sequence, and this process was happening at every position, what frequency of s, Cs, Gs and Ts would we expect after a long time?
29 Worksheet (Rip it off from the back of your packet) Name:! "" # = )*+,-! ". # = )*+,- 1. If the nucleotide is C at time 0, ie P C (0)=1, what is the probability is is C after a long time? If the nucleotide is C at time 0, ie P C (0)=1, what is the probability it is G after a long time? What are the equilibrium nucleotide frequencies we would expect as a result of this process? In other words, if we had a long sequence, and this process was happening at every position, what frequency of s, Cs, Gs and Ts would we expect after a long time? 0.25 each
30 Consider a single nucleotide position ancestor descendant strain 1 descendant strain 2 The probability strain 1 and strain 2 have the same nucleotide at this position I(t) = P 2 (t)+ P2 C (t)+ P2 G (t)+ P2 T (t) Express I(t) in terms of and t. I(t) =
31 Consider a single nucleotide position ancestor descendant strain 1 descendant strain 2 The probability strain 1 and strain 2 have the same nucleotide at this position I(t) = P 2 (t)+ P2 C (t)+ P2 G (t)+ P2 T (t) Express I(t) in terms of and t. " I(t) = % $ # 4 e 4t ' & 2 " % $ # 4 e 4t ' & 2 *Note that this would still be the same if we had imagined the ancestral nucleotide was C, G or T.
32
33 " I(t) = % $ # 4 e 4t ' & 2 " % $ # 4 e 4t ' & 2 I(t) = e 4t e 8t e 4t e 8t I(t) = e 8t I(t) = e 8t
34 Can measure from alignments. 1. Probability two nucleotides are different. p =1 I(t) = e 8t = 3 4 ( 1 e 8t ) 2. Probability of a substitution per site per unit time: 3 Expected number of substitutions per site in one lineage: 3t Expected number of substitutions per site separating the two strains: K = 6t
35
36 4 3 p =1 e 8t e 8t =1 4 3 p " 8t = ln$ 1 4 # 3 p % ' &! = 3 4 ln )
37 Using the Jukes-Cantor correction Partial alignment from the gag gene: SIV_deBrazzaMonkey: TTTCTGGGTT HIV2_human_a: TGT------GCGGT! = 6 13 = Proportion of sites that are different (consider only nongap sites) * = 3 4 ln 1 4 3! = Estimated substitutions per site separating the two strains.
38 Topics for the next few days The HIV genome in context Phylogenetic trees of hosts vs. pathogens: introducing the HIV/SIV case Phylogenetic reconstruction methods Constructing a distance matrix between sequences What is a sequence alignment? The Jukes-Cantor correction The neighbor-joining algorithm to make a tree from distances
39 Hand in your worksheet please! (and be sure you put your full name on it)
EVOLUTIONARY 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 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 informationUnderstanding relationship between homologous sequences
Molecular Evolution Molecular Evolution How and when were genes and proteins created? How old is a gene? How can we calculate the age of a gene? How did the gene evolve to the present form? What selective
More informationMassachusetts Institute of Technology Computational Evolutionary Biology, Fall, 2005 Notes for November 7: Molecular evolution
Massachusetts Institute of Technology 6.877 Computational Evolutionary Biology, Fall, 2005 Notes for November 7: Molecular evolution 1. Rates of amino acid replacement The initial motivation for the neutral
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 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 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 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 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 informationMETHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.
Chapter 12 (Strikberger) Molecular Phylogenies and Evolution METHODS FOR DETERMINING PHYLOGENY In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Modern
More informationWhat Is Conservation?
What Is Conservation? Lee A. Newberg February 22, 2005 A Central Dogma Junk DNA mutates at a background rate, but functional DNA exhibits conservation. Today s Question What is this conservation? Lee A.
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 informationBio 1B Lecture Outline (please print and bring along) Fall, 2007
Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution
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 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 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 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 informationMULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE
MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE Manmeet Kaur 1, Navneet Kaur Bawa 2 1 M-tech research scholar (CSE Dept) ACET, Manawala,Asr 2 Associate Professor (CSE Dept) ACET, Manawala,Asr
More informationEvolutionary Models. Evolutionary Models
Edit Operators In standard pairwise alignment, what are the allowed edit operators that transform one sequence into the other? Describe how each of these edit operations are represented on a sequence alignment
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 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 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 informationReading for Lecture 13 Release v10
Reading for Lecture 13 Release v10 Christopher Lee November 15, 2011 Contents 1 Evolutionary Trees i 1.1 Evolution as a Markov Process...................................... ii 1.2 Rooted vs. Unrooted Trees........................................
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 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 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 information进化树构建方法的概率方法 第 4 章 : 进化树构建的概率方法 问题介绍. 部分 lid 修改自 i i f l 的 ih l i
第 4 章 : 进化树构建的概率方法 问题介绍 进化树构建方法的概率方法 部分 lid 修改自 i i f l 的 ih l i 部分 Slides 修改自 University of Basel 的 Michael Springmann 课程 CS302 Seminar Life Science Informatics 的讲义 Phylogenetic Tree branch internal node
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 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 informationI519 Introduction to Bioinformatics, Genome Comparison. Yuzhen Ye School of Informatics & Computing, IUB
I519 Introduction to Bioinformatics, 2015 Genome Comparison Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Whole genome comparison/alignment Build better phylogenies Identify polymorphism
More informationProcesses of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
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 informationInferring Phylogenetic Trees. Distance Approaches. Representing distances. in rooted and unrooted trees. The distance approach to phylogenies
Inferring Phylogenetic Trees Distance Approaches Representing distances in rooted and unrooted trees The distance approach to phylogenies given: an n n matrix M where M ij is the distance between taxa
More informationChapter 7: Models of discrete character evolution
Chapter 7: Models of discrete character evolution pdf version R markdown to recreate analyses Biological motivation: Limblessness as a discrete trait Squamates, the clade that includes all living species
More informationStochastic processes and
Stochastic processes and Markov chains (part II) Wessel van Wieringen w.n.van.wieringen@vu.nl wieringen@vu nl Department of Epidemiology and Biostatistics, VUmc & Department of Mathematics, VU University
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 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 informationBioinformatics course
Bioinformatics course Phylogeny and Comparative genomics 10/23/13 1 Contents-phylogeny Introduction-biology, life classificationtaxonomy Phylogenetic-tree of life, tree representation Why study phylogeny?
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 informationEarly History up to Schedule. Proteins DNA & RNA Schwann and Schleiden Cell Theory Charles Darwin publishes Origin of Species
Schedule Bioinformatics and Computational Biology: History and Biological Background (JH) 0.0 he Parsimony criterion GKN.0 Stochastic Models of Sequence Evolution GKN 7.0 he Likelihood criterion GKN 0.0
More informationBMI/CS 776 Lecture #20 Alignment of whole genomes. Colin Dewey (with slides adapted from those by Mark Craven)
BMI/CS 776 Lecture #20 Alignment of whole genomes Colin Dewey (with slides adapted from those by Mark Craven) 2007.03.29 1 Multiple whole genome alignment Input set of whole genome sequences genomes diverged
More informationSubstitution = Mutation followed. by Fixation. Common Ancestor ACGATC 1:A G 2:C A GAGATC 3:G A 6:C T 5:T C 4:A C GAAATT 1:G A
GAGATC 3:G A 6:C T Common Ancestor ACGATC 1:A G 2:C A Substitution = Mutation followed 5:T C by Fixation GAAATT 4:A C 1:G A AAAATT GAAATT GAGCTC ACGACC Chimp Human Gorilla Gibbon AAAATT GAAATT GAGCTC ACGACC
More informationQ1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate.
OEB 242 Exam Practice Problems Answer Key Q1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate. First, recall
More informationCladistics and Bioinformatics Questions 2013
AP Biology Name Cladistics and Bioinformatics Questions 2013 1. The following table shows the percentage similarity in sequences of nucleotides from a homologous gene derived from five different species
More informationStochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions
PLGW05 Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions 1 joint work with Ilan Gronau 2, Shlomo Moran 3, and Irad Yavneh 3 1 2 Dept. of Biological Statistics and Computational
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools. Evaluation. Course Homepage.
CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools Giri Narasimhan ECS 389; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs06.html 1/12/06 CAP5510/CGS5166 1 Evaluation
More informationMolecular Evolution and Phylogenetic Tree Reconstruction
1 4 Molecular Evolution and Phylogenetic Tree Reconstruction 3 2 5 1 4 2 3 5 Orthology, Paralogy, Inparalogs, Outparalogs Phylogenetic Trees Nodes: species Edges: time of independent evolution Edge length
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 information31/10/2012. Human Evolution. Cytochrome c DNA tree
Human Evolution Cytochrome c DNA tree 1 Human Evolution! Primate phylogeny! Primates branched off other mammalian lineages ~65 mya (mya = million years ago) Two types of monkeys within lineage 1. New World
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 informationEvolution by duplication
6.095/6.895 - Computational Biology: Genomes, Networks, Evolution Lecture 18 Nov 10, 2005 Evolution by duplication Somewhere, something went wrong Challenges in Computational Biology 4 Genome Assembly
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 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 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 informationOrganizing Life s Diversity
17 Organizing Life s Diversity section 2 Modern Classification Classification systems have changed over time as information has increased. What You ll Learn species concepts methods to reveal phylogeny
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 informationHow Molecules Evolve. Advantages of Molecular Data for Tree Building. Advantages of Molecular Data for Tree Building
How Molecules Evolve Guest Lecture: Principles and Methods of Systematic Biology 11 November 2013 Chris Simon Approaching phylogenetics from the point of view of the data Understanding how sequences evolve
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 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 informationSequence Analysis '17- lecture 8. Multiple sequence alignment
Sequence Analysis '17- lecture 8 Multiple sequence alignment Ex5 explanation How many random database search scores have e-values 10? (Answer: 10!) Why? e-value of x = m*p(s x), where m is the database
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 informationTree Building Activity
Tree Building Activity Introduction In this activity, you will construct phylogenetic trees using a phenotypic similarity (cartoon microbe pictures) and genotypic similarity (real microbe sequences). For
More informationFUNDAMENTALS OF MOLECULAR EVOLUTION
FUNDAMENTALS OF MOLECULAR EVOLUTION Second Edition Dan Graur TELAVIV UNIVERSITY Wen-Hsiung Li UNIVERSITY OF CHICAGO SINAUER ASSOCIATES, INC., Publishers Sunderland, Massachusetts Contents Preface xiii
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 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 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 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 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 informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
More informationConcepts and Methods in Molecular Divergence Time Estimation
Concepts and Methods in Molecular Divergence Time Estimation 26 November 2012 Prashant P. Sharma American Museum of Natural History Overview 1. Why do we date trees? 2. The molecular clock 3. Local clocks
More informationChapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships
Chapter 26: Phylogeny and the Tree of Life You Must Know The taxonomic categories and how they indicate relatedness. How systematics is used to develop phylogenetic trees. How to construct a phylogenetic
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 informationPlan: Evolutionary trees, characters. Perfect phylogeny Methods: NJ, parsimony, max likelihood, Quartet method
Phylogeny 1 Plan: Phylogeny is an important subject. We have 2.5 hours. So I will teach all the concepts via one example of a chain letter evolution. The concepts we will discuss include: Evolutionary
More informationLecture 8 Multiple Alignment and Phylogeny
Introduction to Bioinformatics for Medical Research Gideon Greenspan gdg@cs.technion.ac.il Lecture 8 Multiple Alignment and Phylogeny Multiple Alignment & Phylogeny Multiple Alignment Scoring Complexity
More informationLecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM)
Bioinformatics II Probability and Statistics Universität Zürich and ETH Zürich Spring Semester 2009 Lecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM) Dr Fraser Daly adapted from
More informationEvolutionary Theory and Principles of Phylogenetics. Lucy Skrabanek ICB, WMC March 19, 2008
Evolutionary Theory and Principles of Phylogenetics Lucy Skrabanek ICB, WMC March 19, 2008 Theory of evolution Evolution: process of change over time 2 competing models Phyletic gradualism Punctuated equilibrium
More informationCLADOGRAMS & GENETIC PHYLOGENIES
CLADOGRAMS & GENETIC PHYLOGENIES INTRODUCTION Taxonomists since Linnaeus have used relative similarities and differences to group species into a taxonomic hierarchy of genera, families, orders, etc. Darwin
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 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 informationGenomes and Their Evolution
Chapter 21 Genomes and Their Evolution PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationModeling Evolution DAVID EPSTEIN CELEBRATION. John Milnor. Warwick University, July 14, Stony Brook University
Modeling Evolution John Milnor Stony Brook University DAVID EPSTEIN CELEBRATION Warwick University, July 14, 2007 A First Model for Evolution: The Phylogenetic Tree, U time V W X A B C D E F G 1500 1000
More informationConstructing Evolutionary Trees
Constructing Evolutionary Trees 0-0 HIV Evolutionary Tree SIVs (monkeys)! HIV (human)! human infection! human HIV/M human HIV/M chimpanzee SIV chimpanzee SIV human HIV/N human HIV/N chimpanzee SIV chimpanzee
More informationCluster Analysis of Gene Expression Microarray Data. BIOL 495S/ CS 490B/ MATH 490B/ STAT 490B Introduction to Bioinformatics April 8, 2002
Cluster Analysis of Gene Expression Microarray Data BIOL 495S/ CS 490B/ MATH 490B/ STAT 490B Introduction to Bioinformatics April 8, 2002 1 Data representations Data are relative measurements log 2 ( red
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 informationMolecular Evolution & Phylogenetics Traits, phylogenies, evolutionary models and divergence time between sequences
Molecular Evolution & Phylogenetics Traits, phylogenies, evolutionary models and divergence time between sequences Basic Bioinformatics Workshop, ILRI Addis Ababa, 12 December 2017 1 Learning Objectives
More informationThe Phylogenetic Handbook
The Phylogenetic Handbook A Practical Approach to DNA and Protein Phylogeny Edited by Marco Salemi University of California, Irvine and Katholieke Universiteit Leuven, Belgium and Anne-Mieke Vandamme Rega
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 informationCHAPTER : Prokaryotic Genetics
CHAPTER 13.3 13.5: Prokaryotic Genetics 1. Most bacteria are not pathogenic. Identify several important roles they play in the ecosystem and human culture. 2. How do variations arise in bacteria considering
More information7. Tests for selection
Sequence analysis and genomics 7. Tests for selection Dr. Katja Nowick Group leader TFome and Transcriptome Evolution Bioinformatics group Paul-Flechsig-Institute for Brain Research www. nowicklab.info
More informationSUPPLEMENTARY METHODS
SUPPLEMENTARY METHODS M1: ALGORITHM TO RECONSTRUCT TRANSCRIPTIONAL NETWORKS M-2 Figure 1: Procedure to reconstruct transcriptional regulatory networks M-2 M2: PROCEDURE TO IDENTIFY ORTHOLOGOUS PROTEINSM-3
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 informationSome of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!
Some of these slides 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 informationQuantifying sequence similarity
Quantifying sequence similarity Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, February 16 th 2016 After this lecture, you can define homology, similarity, and identity
More informationDrosophila melanogaster and D. simulans, two fruit fly species that are nearly
Comparative Genomics: Human versus chimpanzee 1. Introduction The chimpanzee is the closest living relative to humans. The two species are nearly identical in DNA sequence (>98% identity), yet vastly different
More informationMaximum Likelihood Until recently the newest method. Popularized by Joseph Felsenstein, Seattle, Washington.
Maximum Likelihood This presentation is based almost entirely on Peter G. Fosters - "The Idiot s Guide to the Zen of Likelihood in a Nutshell in Seven Days for Dummies, Unleashed. http://www.bioinf.org/molsys/data/idiots.pdf
More informationBIOINFORMATICS LAB AP BIOLOGY
BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to
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 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 informationBIOINFORMATICS TRIAL EXAMINATION MASTERS KT-OR
BIOINFORMATICS KT Maastricht University Faculty of Humanities and Science Knowledge Engineering Study TRIAL EXAMINATION MASTERS KT-OR Examiner: R.L. Westra Date: March 30, 2007 Time: 13:30 15:30 Place:
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 information