BINF6201/8201. Molecular phylogenetic methods

Size: px
Start display at page:

Download "BINF6201/8201. Molecular phylogenetic methods"

Transcription

1 BINF60/80 Molecular phylogenetic methods

2 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics is the study of the evolutionary relationships of a group of organisms. Ø The evolutionary relationships of organisms are usually described by the means of a phylogenetic tree. Ø harles arwin s tree of life: The first conceptual evolutionary tree of life.

3 Molecular phylogenetics Ø Ernst Haeckel s tree of organisms was based on the similarity of morphological features of organisms. Ø With the availability of protein and NA sequences, phylogenetic trees are constructed based on the relationships of these sequences. Ø The studies that use molecular sequences to deduce the evolutionary relationships among organisms and genes is called molecular phylogenetics. Ø There are good reasons for using molecular sequence data to study phylogenetics:. Sequences evolve in a more regular manner than do other features;. Sequences are more amenable to quantitative treatment. 3. Sequence data are more abundant. Ernst Haeckel, Stem-Tree of Organisms, 866, courtesy Robert J. Richards

4 Phylogenetic trees Ø A phylogenetic tree is an acyclic (no loop is allowed) graph, in which nodes denote taxonomic units (organism, molecular sequences), and branches (edges) connecting the nodes denote the relationships of the taxonomic units in terms of descent and ancestry. Ø The length of an edge usually reflects the number of evolutionary changes or time of divergence between the two taxonomic units. Ø Phylogenetic trees are usually binary trees: there is no more than three edges connecting a node. Ø If a node has more than one edge connecting to it, it is called an internal node, otherwise it is called an external node or a leaf. Ø Internal nodes represent ancestral taxonomic units, external nodes or leaves represent the extant taxonomic units, and are also referred to as operational taxonomic units (OTUs).

5 Phylogenetic trees Ø Edges that connect to external nodes are called external or peripheral edges, and those that connect internal nodes are called internal edges. Ø If we know the earliest branded edge, which is called an outgroup, we can place a root on the edge connecting the outgroup, then the tree is a rooted tree. Ø The root represents the common ancestor of the OTUs. From the root we can find an evolutionary path to the OUT. Ø The branching pattern of a tree is called its topology. Rotating a tree around its internal nodes does not change its topology. Outgroup Ø If we know or if we can deduce the time of divergence between organisms, then the OTUs will line up level on the same line representing the current time, and vertical length between the two nodes represent the time of their divergence. Rotate around the root by80

6 Phylogenetic trees Ø A tree is said to be additive if the distance between any two OTUs on the tree is equal to the sum of the length of all the branches connecting them. A F I G 6 E For example, if additivity holds, then the distance between A and is = 8 Ø The distance between two OTUs as well as the branch lengths on the tree are estimated from the relationships of the OTUs according to certain rules, so the additivity may not necessarily hold for trees generated by some algorithms. 3 H B

7 Phylogenetic trees Ø If the branch length on a rooted tree is the time of divergence, then for any three OTUs, two branches among them is longer than the third, and the two longest distances are the same. This property of such a tree is called ultrametricity. Ø An ultrametric tree is also additive, but the reverse is not necessarily true. Ø If we use the number of changes (or evolutionary distance) to scale the edges, the OTUs may not necessarily line up level on the same line, because the rates of evolution of different taxonomic units may be different. So the tree is not ultrametric, however, if the tree is rooted, we still know the order of branching during the course of evolution. Ø If the evolutionary rates are the same, then the OTUs will line up level on the same line, and the evolutionary distances can be converted to time of divergence using the same scaling factor. In this case, the tree is ultrametric.

8 Urooted trees Ø If we do not known the earliest branch in the tree, the tree is unrooted. Ø An unrooted tree can only specify the relationships among the OTUs, but does not define an evolutionary path of an OTU. Ø Most phylogenetic tree construction methods produce unrooted trees. Ø To convert an unrooted tree to a rooted one, we usually include an outgroup for the analysis. Ø An outgroup can be identified according to other information, such as paleontological evidence, and morphological evidence. The root is placed on the edge that connects the outgroup and the other OTUs. Outgroup Unrooted tree Rooted tree

9 Monophyletic groups and clades Ø The collection of all the descendants of an ancestor is called a monophyletic group or a clade. Ø A group of OTUs that do not include all the descendants of a common ancestor is called a paraphyletic group. Ø The OTUs A and B form a monophyletic groups; A, B,, and E is a monophyletic group; and is a monophyletic group. Ø A and is paraphyletic group; A, B and E is paraphyletic group; and B and is paraphyletic group, etc. I G 6 3 F H A B E

10 Gene trees and species tree Ø When we construct a phylogenetic tree of a group of genes, the tree reflects the evolutionary relationships of the genes, and it is called a gene tree. Ø The phylogenetic tree that describes the evolutionary relationships of a group of organisms is called a species tree. Ø When we want to infer the species tree of a group of organisms using molecular sequence data, we pick up the gene or genes that are most informative about the evolutionary history of the organisms, and use the constructed gene tree to represent the species tree. The first gene trees were based on cytochromes c and hemoglobin sequences. The widely accepted species trees of organisms are based on the small subunit of ribosomal RNA (rrna) gene sequences, since all organisms have the genes, and they tend to evolve slowly.

11 Methods for phylogenetic tree reconstruction Ø Numerous tree-construction methods have been proposed, because no method performs well under all circumstances. Ø Most of these methods depend on a multiple alignment of the sequences. Ø The gaps in the original multiple alignment will be removed, and sometimes manual adjustments are necessary to remove uncertain alignment in the variable regions. Ø A high quality alignment is necessary for the correct inference of a phylogenetic tree. A multiple alignment of mitochondria rrna genes of some mammals

12 Methods for phylogenetic tree reconstruction Ø These alignment based tree-construction methods can be divided into three categories:. istance matrix methods: evolutionary distance d (number of substitutions/per site per time unit) between each pair of sequences is computed based on a substitution model of sequence evolution, a tree is then constructed by an algorithm based on some functional relationships among the distance values.. Maximum parsimony methods: a tree is constructed through the identification of the tree that confers the shortest path that leads to the changes in the aligned sequences. 3. Maximum likelihood methods: likelihood values for possible trees are computed, and the tree that has the maximal likelihood value is selected as the inferred tree.

13 Unweighted pair-group method with an arithmetic mean (UPGMA) Ø This is the simplest method for tree construction. In order for this method to work correctly, we have to assume that the rate of evolution (rate of substitution) is the same for all lineages so that there is a linear relation between the evolutionary distance and the time of divergence. Ø After obtaining a multiple alignment, we first compute the evolutionary distance d between any pair of sequences based on a sequence substitution model, i.e., J- and KP models, etc. The J- distance matrix of the small subunit mitochondrial rrna genes in a group of catarrhini

14 The UPGMA algorithm Ø We have discussed the UPGMA algorithm earlier, here is its adaptation to constructing a phylogenetic tree: Step : Assign each OUT as a distinct cluster; Step : Join two clusters that have the shortest distance, the length of the branch equals the distance between the two clusters, put branching point at the middle of the branch; Step 3: Re-compute the similarity scores among the clusters if their similarity scores have not been computed as the average pairwise distances, d AB = N N A N A N B i= j= Step 4: Repeat steps and 3 until all OUTs have been linked to another cluster. B d ij

15 The UPGMA algorithm Ø Let s first look at a toy example: A B A B d AB d A d A d AB d B d B d A d B d d d ( AB) ( AB) = ( d = ( d A A + d + d B B ) (AB) ) (AB) d (AB) d (AB) d (AB) d (AB) d d d A d B d If d AB is the smallest, join AB, and put a branching point at the middle of the edge A d AB B If d (AB) is the smallest, join (AB) and, and put a branching point at the middle of the edge A d ( AB) B

16 (AB) (AB) d (AB) d (AB) d (AB) The UPGMA algorithm d d = ( AB) ( d 3 A + d B + d ) (AB) (AB) d (AB) d (AB) d (AB) d If d (AB) is the smallest, join (AB) and, and put a branching point at the middle of the edge d ( AB) A B Join (AB) and, and put a root at the middle of the edge Root d ( AB) A B

17 The UPGMA algorithm Ø The tree constructed by the UPGMA method is rooted, the root is put on the middle point of the last joined cluster. Ø The UPGMA tree is ultrametric: i.e., given any three OTUs, the two longest distances among them are the same. Ø A distance matrix is said to be ultrametric if an ultrametric tree can be constructed such that the distance between any two OTUs on the tree is the same as that specified in the matrix. Ø If the distance matrix is ultrametric, then, UPGMA guarantees to produce a correct tree, i.e., d tree ij = d ij. Ø However, in reality the ultrametricity may not hold, as the sequences may evolve at different rates. Ø Even if the sequences evolve at the same rate, the distances among them will be only approximately ultrametric, because of the random nature of nucleotide substitutions. Ø When the distance matrix is far away from ultrametric, the resulting tree will be very different from the true tree, i.e., d tree ij d ij.

18 The UPGMA algorithm Ø An real-world example: mitochondria rrna genes of a group of closely related atarrhini: A Ø The algorithm first joint chimpanzee and pygmy chimp, and then add Human, and so on. B Ø The tree is ultrametric and hence additive, but the matrix is only approximately ultrametric, so the tree is not very accurate.. d AB = x = 0.73

"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky

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 information

Theory of Evolution Charles Darwin

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

More information

What is Phylogenetics

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)

More information

Algorithms in Bioinformatics

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

More information

Phylogeny: building the tree of life

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

More information

Evolutionary Tree Analysis. Overview

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

More information

Constructing Evolutionary/Phylogenetic Trees

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

More information

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 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 information

Theory of Evolution. Charles Darwin

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 information

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics

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

More information

Multiple Sequence Alignment. Sequences

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

More information

Lecture 11 Friday, October 21, 2011

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

More information

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

More information

Phylogenetic Trees. Phylogenetic Trees Five. Phylogeny: Inference Tool. Phylogeny Terminology. Picture of Last Quagga. Importance of Phylogeny 5.

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

More information

UoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)

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

More information

Phylogenetics: Building Phylogenetic Trees

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

More information

Page 1. Evolutionary Trees. Why build evolutionary tree? Outline

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

More information

8/23/2014. Phylogeny and the Tree of Life

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

More information

Phylogenetics: Building Phylogenetic Trees. COMP Fall 2010 Luay Nakhleh, Rice University

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

More information

Phylogeny and Evolution. Gina Cannarozzi ETH Zurich Institute of Computational Science

Phylogeny and Evolution. Gina Cannarozzi ETH Zurich Institute of Computational Science Phylogeny and Evolution Gina Cannarozzi ETH Zurich Institute of Computational Science History Aristotle (384-322 BC) classified animals. He found that dolphins do not belong to the fish but to the mammals.

More information

CHAPTERS 24-25: Evidence for Evolution and Phylogeny

CHAPTERS 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 information

How to read and make phylogenetic trees Zuzana Starostová

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

More information

C3020 Molecular Evolution. Exercises #3: Phylogenetics

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

More information

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 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 information

Chapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships

Chapter 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 information

Phylogenetics: Distance Methods. COMP Spring 2015 Luay Nakhleh, Rice University

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

More information

Molecular 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 - 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 information

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

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:

More information

Molecular Evolution and Phylogenetic Tree Reconstruction

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

More information

EVOLUTIONARY DISTANCES

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

Phylogenetic Tree Reconstruction

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

More information

Cladistics and Bioinformatics Questions 2013

Cladistics 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 information

Michael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D

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

More information

A (short) introduction to phylogenetics

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

More information

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 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 information

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 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 information

Phylogenetic trees 07/10/13

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

More information

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. 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 information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

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

More information

Dr. Amira A. AL-Hosary

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

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

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

More information

PHYLOGENY & THE TREE OF LIFE

PHYLOGENY & 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 information

Molecular Phylogenetics (part 1 of 2) Computational Biology Course João André Carriço

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)

More information

Microbial Diversity and Assessment (II) Spring, 2007 Guangyi Wang, Ph.D. POST103B

Microbial Diversity and Assessment (II) Spring, 2007 Guangyi Wang, Ph.D. POST103B Microbial Diversity and Assessment (II) Spring, 007 Guangyi Wang, Ph.D. POST03B guangyi@hawaii.edu http://www.soest.hawaii.edu/marinefungi/ocn403webpage.htm General introduction and overview Taxonomy [Greek

More information

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT

Inferring 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 information

Phylogenetic inference

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

More information

Phylogeny 9/8/2014. Evolutionary Relationships. Data Supporting Phylogeny. Chapter 26

Phylogeny 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 information

CS5263 Bioinformatics. Guest Lecture Part II Phylogenetics

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

More information

AP Biology. Cladistics

AP Biology. Cladistics Cladistics Kingdom Summary Review slide Review slide Classification Old 5 Kingdom system Eukaryote Monera, Protists, Plants, Fungi, Animals New 3 Domain system reflects a greater understanding of evolution

More information

C.DARWIN ( )

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

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

THEORY. Based on sequence Length According to the length of sequence being compared it is of following two types

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

More information

Reconstructing the history of lineages

Reconstructing the history of lineages Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics

More information

CSCI1950 Z Computa4onal Methods for Biology Lecture 5

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

More information

Introduction to characters and parsimony analysis

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

More information

Macroevolution Part I: Phylogenies

Macroevolution Part I: Phylogenies Macroevolution Part I: Phylogenies Taxonomy Classification originated with Carolus Linnaeus in the 18 th century. Based on structural (outward and inward) similarities Hierarchal scheme, the largest most

More information

Phylogenetics. BIOL 7711 Computational Bioscience

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

More information

ELE4120 Bioinformatics Tutorial 8

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

More information

PHYLOGENY AND SYSTEMATICS

PHYLOGENY AND SYSTEMATICS AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

Phylogenetic Analysis

Phylogenetic Analysis Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)

More information

Chapter 26 Phylogeny and the Tree of Life

Chapter 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 information

Biology 211 (2) Week 1 KEY!

Biology 211 (2) Week 1 KEY! Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of

More information

Phylogeny. November 7, 2017

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

More information

9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)

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

More information

Constructing Evolutionary/Phylogenetic Trees

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

More information

Phylogeny and the Tree of Life

Phylogeny 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 information

Phylogenetic inference: from sequences to trees

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

More information

Chapter 26: Phylogeny and the Tree of Life

Chapter 26: Phylogeny and the Tree of Life Chapter 26: Phylogeny and the Tree of Life 1. Key Concepts Pertaining to Phylogeny 2. Determining Phylogenies 3. Evolutionary History Revealed in Genomes 1. Key Concepts Pertaining to Phylogeny PHYLOGENY

More information

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. 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

More information

Bioinformatics 1. Sepp Hochreiter. Biology, Sequences, Phylogenetics Part 4. Bioinformatics 1: Biology, Sequences, Phylogenetics

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

More information

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

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

More information

Phylogeny and Molecular Evolution. Introduction

Phylogeny and Molecular Evolution. Introduction Phylogeny and Molecular Evolution Introduction 1 2/62 3/62 Credit Serafim Batzoglou (UPGMA slides) http://www.stanford.edu/class/cs262/slides Notes by Nir Friedman, Dan Geiger, Shlomo Moran, Ron Shamir,

More information

Phylogeny: traditional and Bayesian approaches

Phylogeny: traditional and Bayesian approaches Phylogeny: traditional and Bayesian approaches 5-Feb-2014 DEKM book Notes from Dr. B. John Holder and Lewis, Nature Reviews Genetics 4, 275-284, 2003 1 Phylogeny A graph depicting the ancestor-descendent

More information

Algorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004,

Algorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004, Tracing the Evolution of Numerical Phylogenetics: History, Philosophy, and Significance Adam W. Ferguson Phylogenetic Systematics 26 January 2009 Inferring Phylogenies Historical endeavor Darwin- 1837

More information

molecular evolution and phylogenetics

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

More information

Plan: Evolutionary trees, characters. Perfect phylogeny Methods: NJ, parsimony, max likelihood, Quartet method

Plan: 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 information

Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley

Integrative Biology 200 PRINCIPLES OF PHYLOGENETICS Spring 2018 University of California, Berkeley Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;

More information

Phylogeny and the Tree of Life

Phylogeny 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 information

CHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny

CHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny CHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny To trace phylogeny or the evolutionary history of life, biologists use evidence from paleontology, molecular data, comparative

More information

Classification and Phylogeny

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

More information

Classification, Phylogeny yand Evolutionary History

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

More information

Phylogenetic Networks, Trees, and Clusters

Phylogenetic Networks, Trees, and Clusters Phylogenetic Networks, Trees, and Clusters Luay Nakhleh 1 and Li-San Wang 2 1 Department of Computer Science Rice University Houston, TX 77005, USA nakhleh@cs.rice.edu 2 Department of Biology University

More information

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

Bioinformatics 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

How should we organize the diversity of animal life?

How 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 information

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

(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

More information

Bioinformatics tools for phylogeny and visualization. Yanbin Yin

Bioinformatics 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 information

Lecture 6 Phylogenetic Inference

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,

More information

METHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.

METHODS 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 information

Reading for Lecture 13 Release v10

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........................................

More information

Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies

Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies Bayesian Inference using Markov Chain Monte Carlo in Phylogenetic Studies 1 What is phylogeny? Essay written for the course in Markov Chains 2004 Torbjörn Karfunkel Phylogeny is the evolutionary development

More information

Chapter 26 Phylogeny and the Tree of Life

Chapter 26 Phylogeny and the Tree of Life Chapter 26 Phylogeny and the Tree of Life Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence

More information

Classification and Phylogeny

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

More information

Lecture V Phylogeny and Systematics Dr. Kopeny

Lecture V Phylogeny and Systematics Dr. Kopeny Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437

More information

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? 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 information

Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline

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

More information

RECOVERING NORMAL NETWORKS FROM SHORTEST INTER-TAXA DISTANCE INFORMATION

RECOVERING NORMAL NETWORKS FROM SHORTEST INTER-TAXA DISTANCE INFORMATION RECOVERING NORMAL NETWORKS FROM SHORTEST INTER-TAXA DISTANCE INFORMATION MAGNUS BORDEWICH, KATHARINA T. HUBER, VINCENT MOULTON, AND CHARLES SEMPLE Abstract. Phylogenetic networks are a type of leaf-labelled,

More information

Need for systematics. Applications of systematics. Linnaeus plus Darwin. Approaches in systematics. Principles of cladistics

Need for systematics. Applications of systematics. Linnaeus plus Darwin. Approaches in systematics. Principles of cladistics Topics Need for systematics Applications of systematics Linnaeus plus Darwin Approaches in systematics Principles of cladistics Systematics pp. 474-475. Systematics - Study of diversity and evolutionary

More information

Intraspecific gene genealogies: trees grafting into networks

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

More information

Phylogenies & 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? 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 information