Phylogenetic Trees  Importance of phylogenetic trees  What is the phylogenetic analysis  Example of cladistics  Assumptions in cladistics  Frequently.

Slides:

Advertisements

Similar presentations

Phylogenetic Tree A Phylogeny (Phylogenetic tree) or Evolutionary tree represents the evolutionary relationships among a set of organisms or groups of.

Advertisements

1 General Phylogenetics Points that will be covered in this presentation Tree TerminologyTree Terminology General Points About Phylogenetic TreesGeneral.

Phylogenetic Trees Understand the history and diversity of life. Systematics. –Study of biological diversity in evolutionary context. –Phylogeny is evolutionary.

Phylogenetics - Distance-Based Methods CIS 667 March 11, 2204.

BIO2093 – Phylogenetics Darren Soanes Phylogeny I.

Phylogenetic reconstruction

Molecular Evolution Revised 29/12/06

Lecture 7 – Algorithmic Approaches Justification: Any estimate of a phylogenetic tree has a large variance. Therefore, any tree that we can demonstrate.

BIOE 109 Summer 2009 Lecture 4- Part II Phylogenetic Inference.

Chapter 2 Opener How do we classify organisms?. Figure 2.1 Tracing the path of evolution to Homo sapiens from the universal ancestor of all life.

Building Phylogenies Distance-Based Methods. Methods Distance-based Parsimony Maximum likelihood.

Phylogenetic Analysis. 2 Phylogenetic Analysis Overview Insight into evolutionary relationships Inferring or estimating these evolutionary relationships.

Phylogeny & The Tree of Life. Phylogeny  The evolutionary history of a species or group of species.

Phylogenetic trees Sushmita Roy BMI/CS 576

Phylogenetic Analysis

Multiple Sequence Alignments and Phylogeny.  Within a protein sequence, some regions will be more conserved than others. As more conserved,

Phylogenetic analyses Kirsi Kostamo. The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among.

Phylogenetic Analysis. 2 Introduction Intension –Using powerful algorithms to reconstruct the evolutionary history of all know organisms. Phylogenetic.

Terminology of phylogenetic trees

Molecular phylogenetics

Christian M Zmasek, PhD 15 June 2010.

Molecular evidence for endosymbiosis Perform blastp to investigate sequence similarity among domains of life Found yeast nuclear genes exhibit more sequence.

Phylogenetics Alexei Drummond. CS Friday quiz: How many rooted binary trees having 20 labeled terminal nodes are there? (A) (B)

1 Dan Graur Molecular Phylogenetics Molecular phylogenetic approaches: 1. distance-matrix (based on distance measures) 2. character-state.

plants animals monera fungi protists protozoa invertebrates vertebrates mammals Five kingdom system (Haeckel, 1879)

Phylogenetic Analysis. General comments on phylogenetics Phylogenetics is the branch of biology that deals with evolutionary relatedness Uses some measure.

BINF6201/8201 Molecular phylogenetic methods

Phylogenetics and Coalescence Lab 9 October 24, 2012.

Bioinformatics 2011 Molecular Evolution Revised 29/12/06.

Applied Bioinformatics Week 8 Jens Allmer. Practice I.

Introduction to Phylogenetic Trees

Building phylogenetic trees. Contents Phylogeny Phylogenetic trees How to make a phylogenetic tree from pairwise distances  UPGMA method (+ an example)

Lecture 2: Principles of Phylogenetics

Introduction to Phylogenetics

Calculating branch lengths from distances. ABC A B C----- a b c.

Algorithms in Computational Biology11Department of Mathematics & Computer Science Algorithms in Computational Biology Building Phylogenetic Trees.

Molecular Phylogeny. 2 Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features.

Phylogenetic Analysis Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics Figures from Higgs & Attwood.

Phylogeny & the Tree of Life

Welcome to Class Define the patterns of evolution.

Classification. Cell Types Cells come in all types of shapes and sizes. Cell Membrane – cells are surrounded by a thin flexible layer Also known as a.

Applied Bioinformatics Week 8 Jens Allmer. Theory I.

Ayesha M.Khan Spring Phylogenetic Basics 2 One central field in biology is to infer the relation between species. Do they possess a common ancestor?

1 CAP5510 – Bioinformatics Phylogeny Tamer Kahveci CISE Department University of Florida.

Chapter 26 Phylogeny and the Tree of Life

Lesson Overview Lesson Overview Modern Evolutionary Classification 18.2.

Phylogenetic trees. 2 Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features.

Phylogeny & Systematics The study of the diversity and relationships among organisms.

Bioinformatics Lecture 3 Molecular Phylogenetic By: Dr. Mehdi Mansouri Mehr 1395.

First & Last Name August X, 2000 Evolution

Phylogeny and the Tree of Life

Introduction to Bioinformatics Resources for DNA Barcoding

Phylogenetic basis of systematics

Systematics and Phylogenetic Revolution

Phylogeny & the Tree of Life

Inferring a phylogeny is an estimation procedure.

Phylogenetic Inference

Multiple Alignment and Phylogenetic Trees

Goals of Phylogenetic Analysis

Cladistics (Ch. 22) Based on phylogenetics – an inferred reconstruction of evolutionary history.

Patterns in Evolution I. Phylogenetic

Chapter 19 Molecular Phylogenetics

Lecture 7 – Algorithmic Approaches

Molecular data assisted morphological analyses

Phylogenetic Trees Jasmin sutkovic.

A bacterial antibiotic resistance gene with eukaryotic origins

Phylogenetic comparison among selected Pasteurella multocida and Haemophilus influenzae species with completed genome sequences. Phylogenetic comparison.

A bacterial antibiotic resistance gene with eukaryotic origins

1 2 Biology Warm Up Day 6 Turn phones in the baskets

Presentation transcript:

Phylogenetic Trees  Importance of phylogenetic trees  What is the phylogenetic analysis  Example of cladistics  Assumptions in cladistics  Frequently used terms  Fundamentals of Phylogenetc models  Phylogenetic software

Importance of Phylogenetic Tree Classification is important to understand Evolutionary history of an Organism Study of Biological Diversity Organization Progressive Multiple Sequence Alignment

What is Phylogenetic Analysis Study of evolutionary relationship Inferring or estimating relationship Usually presented as branching, tree Gene Tree: Inherited relatioships It is also called cladistics clade means branch in Greek Member of group/clade share a common rel.

Example of Cladistics

Assumptions in Cladistics Any group of oragnisms is related by descent from a common ancestor Members of a group or clade share common evolutionary history A group sharing a unique feature, different from other groups There is bifurrcating pattern of cladogenesis Change in charterstics occurs in lineages over time

Frequently Used Terms Clade: A monophyletic taxon. Clades are group of organisms Taxon: Named group or organisms but not necessarily a clade Branch Length: In some case it repersent divergence Node: A bifurcating branch point

Fundamentals of Phylogenetic Models Sequence alignment (AMPS,Clustal-W) Substitution model (weight model) –Rates between Bases –Site Substitution(overall compositional change) Tree building Tree Evaluation

Tree Building Distance Based Methods –UPGMA: Unweighted Pair Group Method It is a Clustring algorithm, it cluster tree branches based on greatest similarity among pairs and averages of joined pairs –NJ: Neighbor Joining First, it join nearest pair in start and then continue till one remain Character-Based –Maximum Parismony (MP) –Maximum Likelihood (ML)

Tree Evaluation Randomize Tree Randomize Character Data Bootstrap Likelihood Test

PHYLIP PAUP PUZZLE TreeDraw MACCLAD Web Based –webphylip, PhyloBlast