Theory of Evolution. Charles Darwin
|
|
- Philip Russell
- 5 years ago
- Views:
Transcription
1 Theory of Evolution harles arwin : 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 to survive and to reproduce. Speciation arises by splitting of one population into subpopulations. Gregor Mendel and his work (856-6) on inheritance. /5/ Lecture
2 /5/ Lecture
3 ominant View of Evolution ll existing organisms are derived from a common ancestor and that new species arise by splitting of a population into subpopulations that do not cross-breed. Organization: irected Rooted Tree; Existing species: Leaves; ommon ancestor species (divergence event): Internal node; Length of an edge: Time. /5/ Lecture
4 Phylogeny /5/ Lecture
5 onstructing Evolutionary/Phylogenetic Trees broad categories: istance-based methods Ultrametric dditive: UPGM Transformed istance Neighbor-Joining haracter-based Maximum Parsimony Maximum Likelihood ayesian Methods /5/ Lecture 5
6 Ultrametric n ultrametric tree: decreasing internal node labels distance between two nodes is label of least common ancestor. n ultrametric distance matrix: Symmetric matrix such that for every i, j, k, there is tie for maximum of (i,j), (j,k), (i,k) ij, ik jk i j k /5/ Lecture 6
7 Ultrametric: ssumptions Molecular lock Hypothesis, Zuckerkandl & Pauling, 96: ccepted point mutations in amino acid sequence of a protein occurs at a constant rate. Varies from protein to protein Varies from one part of a protein to another /5/ Lecture 7
8 Ultrametric ata Sources Lab-based methods: hybridization Take denatured N of the taxa and let them hybridize. Then measure energy to separate. Sequence-based methods: distance /5/ Lecture 8
9 Ultrametric: Example E F G H 5 E F G H E,,F,H,G /5/ Lecture 9 5
10 Ultrametric: Example E F G H 5 5 E F G H 5,G F E H /5/ Lecture
11 /5/ Lecture Ultrametric: istances omputed H G F E 5 5 H G F E,G E 5 F H
12 /5/ Lecture dditive-istance Trees dditive distance trees are edge-weighted trees, with distance between leaf nodes are exactly equal to length of path between nodes
13 Unrooted Trees on Taxa /5/ Lecture
14 Four-Point ondition If the true tree is as shown below, then. d + d < d + d, and. d + d < d + d /5/ Lecture
15 Unweighted pair-group method with arithmetic means (UPGM) d d () d d d () d d d d d () = (d + d ) / d / /5/ Lecture 5
16 Transformed istance Method UPGM makes errors when rate constancy among lineages does not hold. Remedy: introduce an outgroup & make n corrections ko ij' = Now apply UPGM ij io jo + k = n /5/ Lecture 6
17 Saitou & Nei: Neighbor-Joining Method Start with a star topology. Find the pair to separate such that the total length of the tree is minimized. The pair is then replaced by its arithmetic mean, and the process is repeated. S = + ( n ) n ( + + k k k = ( n ) ) i j n ij /5/ Lecture 7
18 /5/ Lecture 8 Neighbor-Joining n n = = n j i ij n k k k n n S ) ( ) ( ) (
19 onstructing Evolutionary/Phylogenetic Trees broad categories: istance-based methods Ultrametric dditive: UPGM Transformed istance Neighbor-Joining haracter-based Maximum Parsimony Maximum Likelihood ayesian Methods /5/ Lecture 9
20 /5/ Lecture haracter-based Methods Input: characters, morphological features, sequences, etc. Output: phylogenetic tree that provides the history of what features changed. [Perfect Phylogeny Problem] one leaf/object, edge per character, path changed traits E 5 5 E
21 Example Perfect phylogeny does not always exist. 5 E /5/ Lecture
22 Maximum Parsimony Minimize the total number of mutations implied by the evolutionary history /5/ Lecture
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 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 informationGel Electrophoresis. 10/28/0310/21/2003 CAP/CGS 5991 Lecture 10Lecture 9 1
Gel Electrophoresis Used to measure the lengths of DNA fragments. When voltage is applied to DNA, different size fragments migrate to different distances (smaller ones travel farther). 10/28/0310/21/2003
More 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 informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More 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 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 informationEvolutionary Tree Analysis. Overview
CSI/BINF 5330 Evolutionary Tree Analysis Young-Rae Cho Associate Professor Department of Computer Science Baylor University Overview Backgrounds Distance-Based Evolutionary Tree Reconstruction Character-Based
More 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 informationPhylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline
Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying
More 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 informationSeuqence Analysis '17--lecture 10. Trees types of trees Newick notation UPGMA Fitch Margoliash Distance vs Parsimony
Seuqence nalysis '17--lecture 10 Trees types of trees Newick notation UPGM Fitch Margoliash istance vs Parsimony Phyogenetic trees What is a phylogenetic tree? model of evolutionary relationships -- common
More 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 informationPhylogenetic 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 information9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)
I9 Introduction to Bioinformatics, 0 Phylogenetic ree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & omputing, IUB Evolution theory Speciation Evolution of new organisms is driven by
More informationCS5238 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
More informationDNA Phylogeny. Signals and Systems in Biology Kushal EE, IIT Delhi
DNA Phylogeny Signals and Systems in Biology Kushal Shah @ EE, IIT Delhi Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics :
More informationPhylogeny: 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 informationGENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS.
!! www.clutchprep.com CONCEPT: OVERVIEW OF EVOLUTION Evolution is a process through which variation in individuals makes it more likely for them to survive and reproduce There are principles to the theory
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 informationCopyright notice. Molecular Phylogeny and Evolution. Goals of the lecture. Introduction. Introduction. December 15, 2008
opyright notice Molecular Phylogeny and volution ecember 5, 008 ioinformatics J. Pevsner pevsner@kennedykrieger.org Many of the images in this powerpoint presentation are from ioinformatics and Functional
More informationInferring 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
More informationAdditive 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 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 informationPhylogeny 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 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 informationMichael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D
7.91 Lecture #5 Database Searching & Molecular Phylogenetics Michael Yaffe B C D B C D (((,B)C)D) Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood
More informationEVOLUTIONARY DISTANCES
EVOLUTIONARY DISTANCES FROM STRINGS TO TREES Luca Bortolussi 1 1 Dipartimento di Matematica ed Informatica Università degli studi di Trieste luca@dmi.units.it Trieste, 14 th November 2007 OUTLINE 1 STRINGS:
More 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 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 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 informationELE4120 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 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 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 informationBuilding 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
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 informationCSCI1950 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 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 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 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 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 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 informationBiology 211 (2) Week 1 KEY!
Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of
More informationHow should we organize the diversity of animal life?
How should we organize the diversity of animal life? The difference between Taxonomy Linneaus, and Cladistics Darwin What are phylogenies? How do we read them? How do we estimate them? Classification (Taxonomy)
More 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 informationPhylogeny. Properties of Trees. Properties of Trees. Trees represent the order of branching only. Phylogeny: Taxon: a unit of classification
Multiple sequence alignment global local Evolutionary tree reconstruction Pairwise sequence alignment (global and local) Substitution matrices Gene Finding Protein structure prediction N structure prediction
More 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 informationConsistency Index (CI)
Consistency Index (CI) minimum number of changes divided by the number required on the tree. CI=1 if there is no homoplasy negatively correlated with the number of species sampled Retention Index (RI)
More 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 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 informationMultiple Sequence Alignment. Sequences
Multiple Sequence Alignment Sequences > YOR020c mstllksaksivplmdrvlvqrikaqaktasglylpe knveklnqaevvavgpgftdangnkvvpqvkvgdqvl ipqfggstiklgnddevilfrdaeilakiakd > crassa mattvrsvksliplldrvlvqrvkaeaktasgiflpe
More informationWhat is Phylogenetics
What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)
More informationInferring 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 informationPhylogeny. Information. ARB-Workshop 14/ CEH Oxford. Molecular Markers. Phylogeny The Backbone of Biology. Why? Zuckerkandl and Pauling 1965
Frank Oliver löckner Information Phylogeny Who are we: Dr. Frank Oliver löckner Dr. Jörg Peplies Max Planck Institute for Marine Microbiology Microbial enomics roup Bremen, ermany ontact: arb@mpibremen.de
More informationPhylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?
Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them? Carolus Linneaus:Systema Naturae (1735) Swedish botanist &
More 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 informationPhylogenetic inference: from sequences to trees
W ESTFÄLISCHE W ESTFÄLISCHE W ILHELMS -U NIVERSITÄT NIVERSITÄT WILHELMS-U ÜNSTER MM ÜNSTER VOLUTIONARY FUNCTIONAL UNCTIONAL GENOMICS ENOMICS EVOLUTIONARY Bioinformatics 1 Phylogenetic inference: from sequences
More informationChapter 3: Phylogenetics
Chapter 3: Phylogenetics 3. Computing Phylogeny Prof. Yechiam Yemini (YY) Computer Science epartment Columbia niversity Overview Computing trees istance-based techniques Maximal Parsimony (MP) techniques
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 informationAnatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses
Anatomy of a tree outgroup: an early branching relative of the interest groups sister taxa: taxa derived from the same recent ancestor polytomy: >2 taxa emerge from a node Anatomy of a tree clade is group
More informationReproduction- passing genetic information to the next generation
166 166 Essential Question: How has biological evolution led to the diversity of life? B-5 Natural Selection Traits that make an organism more or less likely to survive in an environment and reproduce
More informationIntraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation
More informationBioinformatics 1. Sepp Hochreiter. Biology, Sequences, Phylogenetics Part 4. Bioinformatics 1: Biology, Sequences, Phylogenetics
Bioinformatics 1 Biology, Sequences, Phylogenetics Part 4 Sepp Hochreiter Klausur Mo. 30.01.2011 Zeit: 15:30 17:00 Raum: HS14 Anmeldung Kusss Contents Methods and Bootstrapping of Maximum Methods Methods
More 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 informationMacroevolution Part I: Phylogenies
Macroevolution Part I: Phylogenies Taxonomy Classification originated with Carolus Linnaeus in the 18 th century. Based on structural (outward and inward) similarities Hierarchal scheme, the largest most
More 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 informationReconstructing the history of lineages
Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics
More informationEQ: How are genetic variations caused and how do they lead to natural selection?
EQ: How are genetic variations caused and how do they lead to natural selection? What is natural selection Individuals that have physical or behavioral traits that better suit their environment are more
More informationA Phylogenetic Network Construction due to Constrained Recombination
A Phylogenetic Network Construction due to Constrained Recombination Mohd. Abdul Hai Zahid Research Scholar Research Supervisors: Dr. R.C. Joshi Dr. Ankush Mittal Department of Electronics and Computer
More informationPhylogenetics Todd Vision Spring Some applications. Uncultured microbial diversity
Phylogenetics Todd Vision Spring 2008 Tree basics Sequence alignment Inferring a phylogeny Neighbor joining Maximum parsimony Maximum likelihood Rooting trees and measuring confidence Software and file
More informationLab 06 Phylogenetics, part 1
Lab 06 Phylogenetics, part 1 phylogeny is a visual representation of a hypothesis about the relationships among a set of organisms. Phylogenetics is the study of phylogenies and and their development.
More informationEvolutionary 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 informationLab 2A--Life on Earth
Lab 2A--Life on Earth Geology 1402 Chapters 3 & 7 in the textbook 1 A comment Many people including professional scientist are skeptical of evolution or outright reject it. I am not attempting to change
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationNJMerge: 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
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 informationB (a) n = 3 B D C. (b) n = 4
onstruction of Phylogenetic Trees from mino cid Sequences using a Genetic lgorithm Hideo Matsuda matsuda@ics.es.osaka-u.ac.jp epartment of Information and omputer Sciences, Faculty of Engineering Science,
More informationBig Idea #1: The process of evolution drives the diversity and unity of life
BIG IDEA! Big Idea #1: The process of evolution drives the diversity and unity of life Key Terms for this section: emigration phenotype adaptation evolution phylogenetic tree adaptive radiation fertility
More informationChapter 27: Evolutionary Genetics
Chapter 27: Evolutionary Genetics Student Learning Objectives Upon completion of this chapter you should be able to: 1. Understand what the term species means to biology. 2. Recognize the various patterns
More informationPhylogenetic analyses. Kirsi Kostamo
Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,
More 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 informationBIOL 1010 Introduction to Biology: The Evolution and Diversity of Life. Spring 2011 Sections A & B
BIOL 1010 Introduction to Biology: The Evolution and Diversity of Life. Spring 2011 Sections A & B Steve Thompson: stthompson@valdosta.edu http://www.bioinfo4u.net 1 ʻTree of Life,ʼ ʻprimitive,ʼ ʻprogressʼ
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 informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Chapter focus Shifting from the process of how evolution works to the pattern evolution produces over time. Phylogeny Phylon = tribe, geny = genesis or origin
More 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 informationInferring phylogeny. Today s topics. Milestones of molecular evolution studies Contributions to molecular evolution
Today s topics Inferring phylogeny Introduction! Distance methods! Parsimony method!"#$%&'(!)* +,-.'/01!23454(6!7!2845*0&4'9#6!:&454(6 ;?@AB=C?DEF Overview of phylogenetic inferences Methodology Methods
More informationPrinciples of Phylogeny Reconstruction How do we reconstruct the tree of life? Basic Terminology. Looking at Trees. Basic Terminology.
Principles of Phylogeny Reconstruction How do we reconstruct the tree of life? Phylogeny: asic erminology Outline: erminology Phylogenetic tree: Methods Problems parsimony maximum likelihood bootstrapping
More informationThursday, January 14. Teaching Point: SWBAT. assess their knowledge to prepare for the Evolution Summative Assessment. (TOMORROW) Agenda:
Thursday, January 14 Teaching Point: SWBAT. assess their knowledge to prepare for the Evolution Summative Assessment. (TOMORROW) Agenda: 1. Show Hinsz your completed Review WS 2. Discuss answers to Review
More informationIt all depends on barriers that prevent members of two species from producing viable, fertile hybrids.
Name: Date: Theory of Evolution Evolution: Change in a over a period of time Explains the great of organisms Major points of Origin of Species Descent with Modification o All organisms are related through
More informationEvolution of Body Size in Bears. How to Build and Use a Phylogeny
Evolution of Body Size in Bears How to Build and Use a Phylogeny Lesson II Using a Phylogeny Objectives for Lesson II: 1. Overview of concepts 1. Simple ancestral state reconstruction on the bear phylogeny
More informationLecture V Phylogeny and Systematics Dr. Kopeny
Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437
More informationPHYLOGENY AND SYSTEMATICS
AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationComputational Genomics
omputational Genomics Molecular Evolution: Phylogenetic trees Eric Xing Lecture, March, 2007 Reading: DTW boo, hap 2 DEKM boo, hap 7, Phylogeny In, Ernst Haecel coined the word phylogeny and presented
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationBiology 1B Evolution Lecture 2 (February 26, 2010) Natural Selection, Phylogenies
1 Natural Selection (Darwin-Wallace): There are three conditions for natural selection: 1. Variation: Individuals within a population have different characteristics/traits (or phenotypes). 2. Inheritance:
More informationEstimating Evolutionary Trees. Phylogenetic Methods
Estimating Evolutionary Trees v if the data are consistent with infinite sites then all methods should yield the same tree v it gets more complicated when there is homoplasy, i.e., parallel or convergent
More informationSupplementary Information
Supplementary Information For the article"comparable system-level organization of Archaea and ukaryotes" by J. Podani, Z. N. Oltvai, H. Jeong, B. Tombor, A.-L. Barabási, and. Szathmáry (reference numbers
More informationI. Short Answer Questions DO ALL QUESTIONS
EVOLUTION 313 FINAL EXAM Part 1 Saturday, 7 May 2005 page 1 I. Short Answer Questions DO ALL QUESTIONS SAQ #1. Please state and BRIEFLY explain the major objectives of this course in evolution. Recall
More information