Bioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony

Size: px
Start display at page:

Download "Bioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony"

Transcription

1 ioinformatics -- lecture 9 Phylogenetic trees istance-based tree building Parsimony

2 (,(,(,))) rees can be represented in "parenthesis notation". Each set of parentheses represents a branch-point (bifurcation), the comma separates left and right lineages. (,(,(,))) = Parenthesis notation can contain sequence labels too.

3 Evolutionary time ladogram Phylogram Ultrametric tree no meaning genetic change time (:5,(:,(:,:6):):3) parenthesis notation can have both labels and distances.

4 istance metrics MERI ISNES between any two or three taxa (a, b, and c) have the following properties: Property : d (a, b) 0 Non-negativity Property 2: d (a, b) = d (b, a) Symmetry Property 3: d (a, b) = 0 if and only if a = b istinctness Property 4: d (a, c) d (a, b) + d (b, c) riangle inequality a 9 6 b 5 c triangle inequality

5 ULRMERI ISNES...must satisfy the previous four conditions, plus: Property 5 istance metrics he distances from any branch point to the taxa in the clade defined by that branch point are equal a b c If distances are ultrametric, then the sequences are evolving in a perfectly clock-like manner. So any two sequences always have the same distance to their common ancestor.

6 istance metrics dditivity Property 6: Example: if (a,b) are nearest neighbors, d (a, b) + d (c, d) maximum [d (a, c) + d (b, d), d (a, d) + d (b, c)] For distances to fit into an evolutionary tree, they must be additive. Estimated distances often fall short of these criteria, and thus can fail to produce correct evolutionary trees. d (a, b) d (c, d) lineage that goes backwards in time violates additivity.

7 What s wrong with these distances?

8 What s wrong with this tree? 2 6 3

9 id the Florida entist infect his patients with HIV? Phylogenetic tree of HIV sequences from the ENIS, his Patients, & Local HIV-infected People: ENIS Patient Patient Patient G Patient Patient E Patient ENIS Local control 2 Local control 3 Patient F Local control 9 Local control 35 Local control 3 Patient Yes: he HIV sequences from these patients fall within the clade of HIV sequences found in the dentist. No No From Ou et al. (992) and Page & Holmes (998)

10 haracter-based versus distance-based methods for tree building haracter-based methods: Use the aligned sequences directly during tree inference. axa Species Species Species Species Species E haracters GGGG GG GGGG GGGGGG GGGG istance-based methods: ransform the sequence data into pairwise distances, and then use the matrix during tree building, ignoring characters. E Species Species Species Species Species E

11 alculating distances Uncorrected p-distance: count the changes, divide by the length. Species Species Species Species Species E GGGG GG GGGG GGGGGG GGGG op: uncorrected p-distance, ottom: Jukes-antor distance E Species Species Species Species Species E Jukes-antor correction: K(,) = -3/4 ln [ - 4/3 (,)] (,) = 4/20

12 Homoplasy Independent evolution of the same character. () onvergent events (in either related on unrelated entities), (2) Parallel events (in related entities) (3) Reversals (in related entities) G G G G G G G G () (2) (3) he Jukes-antor correction assumes homoplasy occurs at the rate predicted by random mutations.

13 Neighbor joining: a distance-based method hoose the closest neighbors. dd a node between them. hoose the next closest, ad so on. E Species Species Species Species Species E E

14 Neighbor joining: phylogram Finally, adjust the branch lengths to fit the distances, if possible! E Species Species Species Species Species E E

15 Fitch-Margoliash algorithm for calculating the branch lengths. Find the most closely-related pair of sequences, and 2. alculate the average distance from to all other sequences, then from to all other sequences. x x x 3. djust the position of the common ancestor node for and so that the difference between the averages is equal to the difference between the and branch lengths, while the sum of the branch lengths is still equal to d(,). d()-d() = (d(,)+d(,))/2 - (d(,)+d(,))/2 NOE: the difference between the averages may be greater than (,), making step 3 impossible.

16 In class: create a rooted phylogram with 4 taxa GGGGGG GGGGGGG GGGGGG GGGGGG K(,) = -3/4 ln [ - 4/3 pdist(,)] pdist irections:.make a distance matrix. (p-distance, then convert to J- distance) 2.Use Neighbor-joining to make a tree. 3.djust branch lengths using Fitch-Margoliash. 4.hoose the root using the Midpoint method.

17 Which method do I use? Sequence similarity strong weak very weak Method to use distance parsimony maximum likelihood

18 Maximum parsimony -- it's character-building Optimality criterion: he most-parsimonious tree is the one that requires the fewest number of evolutionary events (e.g., nucleotide substitutions, amino acid replacements) to explain the sequences. E GGGG GG GGGG GGGGGG GGGG For this column, and this tree, one mutation event is required.

19 character-based tree-building For this other column, the same tree requires two mutation events. different tree would require only one. E GGGG GG GGGG GGGGGG GGGG

20 Finding the minimum number of mutations Given a tree and a set of taxa, one-letter each () choose optional characters for each ancestor. (2) Select the root character that minimizes the number of mutations by selecting each and propagating it through the tree. // / / / minimum 2 mutations minimum mutation

21 Ignore non-informative sites No mismatchs ---> 0 mutations, all trees mismatch --> mutation, all trees. all different --> all trees equivalent. 2

22 Max Unweighted Parsimony: rying all trees E GGGG GGG GGGG GGGGGG GGGG OLS

Seuqence 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

Constructing 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

Constructing 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

Amira 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

Dr. 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

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

9/30/11. 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

"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

Theory 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

Tree 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

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:

Phylogenetics: 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

Phylogenetics. 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

Phylogenetics: 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

Page 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

Phylogenetic 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

Phylogenetic 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

Phylogeny 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

POPULATION 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

Evolutionary 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

DNA 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 :

Algorithms 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

What 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)

Phylogenetic trees 07/10/13

Phylogenetic trees 07/10/13 A tree is the only figure to occur in On the Origin of Species by Charles Darwin. It is a graphical representation of the evolutionary relationships among entities that share

Copyright 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

Phylogenetic 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

THEORY. 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

Introduction 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

BINF6201/8201. 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

Phylogenetics: 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

Phylogenetic 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

Consistency 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)

C.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

Phylogenetics: 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

Phylogeny. 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

Phylogenetic 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

Michael 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

8/23/2014. 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

Building Phylogenetic Trees UPGMA & NJ

uilding Phylogenetic Trees UPGM & NJ UPGM UPGM Unweighted Pair-Group Method with rithmetic mean Unweighted = all pairwise distances contribute equally. Pair-Group = groups are combined in pairs. rithmetic

Sequence 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

A (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

Phylogenetic 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,

Multiple Sequence Alignment. Sequences

Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe

Lecture 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

Letter to the Editor. Department of Biology, Arizona State University

Letter to the Editor Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well Michael S. Rosenberg and Sudhir Kumar Department of Biology, Arizona

C3020 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

Estimating 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

Bioinformatics 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

Molecular 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

Intraspecific 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

Inferring Molecular Phylogeny

r. Walter Salzburger The tree of life, ustav Klimt (1907) Inferring Molecular Phylogeny Inferring Molecular Phylogeny 2 1. Molecular Markers Inferring Molecular Phylogeny 3 Immunological comparisons! Nuttall

Principles 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

Phylogenetics. 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

CS5263 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

Quantifying 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

Midterm Exam #1. MB 451 Microbial Diversity. Honor pledge: I have neither given nor received unauthorized aid on this test.

Midterm xam #1 M 451 Microbial iversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : ate : Feb 5, 2007 Name : KY 1. What are the three primary evolutionary branches

Thanks 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

CS5238 Combinatorial methods in bioinformatics 2003/2004 Semester 1. Lecture 8: Phylogenetic Tree Reconstruction: Distance Based - October 10, 2003

CS5238 Combinatorial methods in bioinformatics 2003/2004 Semester 1 Lecture 8: Phylogenetic Tree Reconstruction: Distance Based - October 10, 2003 Lecturer: Wing-Kin Sung Scribe: Ning K., Shan T., Xiang

Phylogenetics 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

Additive distances. w(e), where P ij is the path in T from i to j. Then the matrix [D ij ] is said to be additive.

Additive distances Let T be a tree on leaf set S and let w : E R + be an edge-weighting of T, and assume T has no nodes of degree two. Let D ij = e P ij w(e), where P ij is the path in T from i to j. Then

Inferring 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

MOLECULAR EVOLUTION AND PHYLOGENETICS SERGEI L KOSAKOVSKY POND CSE/BIMM/BENG 181 MAY 27, 2011

MOLECULAR EVOLUTION AND PHYLOGENETICS If we could observe evolution: speciation, mutation, natural selection and fixation, we might see something like this: AGTAGC GGTGAC AGTAGA CGTAGA AGTAGA A G G C AGTAGA

Phylogenetic 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

Classification, 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

Molecular 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)

"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

Phylogenetic 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

How 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

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

Phylogeny: 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

Reading 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........................................

Phylogenetics: 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

Is 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;

Classification 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

Anatomy 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

Phylogeny. 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

Lecture 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,

Evolutionary 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

molecular evolution and phylogenetics

molecular evolution and phylogenetics Charlotte Darby Computational Genomics: Applied Comparative Genomics 2.13.18 https://www.thinglink.com/scene/762084640000311296 Internal node Root TIME Branch Leaves

Estimating 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

Classification 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

What 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.

UoN, 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

! A species tree aims at representing the evolutionary relationships between species. ! Species trees and gene trees are generally related...

Bioinformatics Phylogeny Species trees versus molecule tree! A species tree aims at representing the evolutionary relationships between species.! A molecule tree represents the evolutionary history of

Molecular 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

Lecture 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

NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees

NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees Erin Molloy and Tandy Warnow {emolloy2, warnow}@illinois.edu University of Illinois at Urbana

A 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

Phylogene)cs. IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, Joyce Nzioki

Phylogene)cs IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, 2016 Joyce Nzioki Phylogenetics The study of evolutionary relatedness of organisms. Derived from two Greek words:» Phle/Phylon: Tribe/Race» Genetikos:

Phylogenetics 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/

CSCI1950 Z Computa4onal Methods for Biology Lecture 5

CSCI1950 Z Computa4onal Methods for Biology Lecture 5 Ben Raphael February 6, 2009 hip://cs.brown.edu/courses/csci1950 z/ Alignment vs. Distance Matrix Mouse: ACAGTGACGCCACACACGT Gorilla: CCTGCGACGTAACAAACGC

(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise

Bot 421/521 PHYLOGENETIC ANALYSIS I. Origins A. Hennig 1950 (German edition) Phylogenetic Systematics 1966 B. Zimmerman (Germany, 1930 s) C. Wagner (Michigan, 1920-2000) II. Characters and character states

Molecular 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

Reconstructing Evolutionary Trees. Chapter 14

Reconstructing Evolutionary Trees Chapter 14 Phylogenetic trees The evolutionary history of a group of species = phylogeny The problem: Evolutionary histories can never truly be known. Once again, we are

Evolutionary trees. Describe the relationship between objects, e.g. species or genes

Evolutionary trees Bonobo Chimpanzee Human Neanderthal Gorilla Orangutan Describe the relationship between objects, e.g. species or genes Early evolutionary studies The evolutionary relationships between

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)

ELE4120 Bioinformatics Tutorial 8

ELE4120 ioinformatics Tutorial 8 ontent lassifying Organisms Systematics and Speciation Taxonomy and phylogenetics Phenetics versus cladistics Phylogenetic trees iological classification Goal: To develop

Understanding 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