Trees as a Tool to Visualize Evolutionary History

Slides:

Advertisements

Similar presentations

Reading Phylogenetic Trees Gloria Rendon NCSA November, 2008.

Advertisements

Introduction to Phylogenies

The History of Classification Out of this concept was developed the "scale of nature" idea that suggested living things were arranged on a scale of perfection,

No similarity vs no homology If two (complex) sequences show significant similarity in their primary sequence, they have shared ancestry, and probably.

Lecture 23: Introduction to Coalescence April 7, 2014.

Modern Evolutionary Classification Section Which Similarities are Most Important? Taxonomic groups above species were “invented” to distinguish.

Plant Molecular Systematics (Phylogenetics). Systematics classifies species based on similarity of traits and possible mechanisms of evolution, a change.

Phylogenetic reconstruction

Cladograms Introduction to Cladograms. Student Goals and CA Standards Goals CA Standards.

Molecular Evolution Revised 29/12/06

Trees and Sequence Space J. Peter Gogarten University of Connecticut Dept. of Molecular and Cell Biology Sculpture at Royal Botanical Gardens, Kew.

Branches, splits, bipartitions In a rooted tree: clades (for urooted trees sometimes the term clann is used) Mono-, Para-, polyphyletic groups, cladists.

Example of bipartition analysis for five genomes of photosynthetic bacteria (188 gene families) total 10 bipartitions R: Rhodobacter capsulatus, H: Heliobacillus.

CHAPTER 25 TRACING PHYLOGENY. I. PHYLOGENY AND SYSTEMATICS A.TAXONOMY EMPLOYS A HIERARCHICAL SYSTEM OF CLASSIFICATION  SYSTEMATICS, THE STUDY OF BIOLOGICAL.

Gene transfer Organismal tree: species B species A species C species D Gene Transfer seq. from B seq. from A seq. from C seq. from D molecular tree: speciation.

Cenancestor (aka MRCA or LUCA) as placed by ancient duplicated genes (ATPases, Signal recognition particles, EF) The “Root” strictly bifurcating no reticulation.

Cenancestor (aka LUCA or MRCA) can be placed using the echo remaining from the early expansion of the genetic code. reflects only a single cellular component.

Branches, splits, bipartitions In a rooted tree: clades Mono-, Para-, polyphyletic groups, cladists and a natural taxonomy Terminology The term cladogram.

BIOE 109 Evolution Summer 2009 Lecture 2- Part II Formulation of theory of natural selection.

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.

Protein structure:. Angles in the protein backbone.

Trees? J. Peter Gogarten University of Connecticut Dept. of Molecular and Cell Biology Sculpture at Royal Botanical Gardens, Kew.

MCB 372 #14: Student Presentations, Discussion, Clustering Genes Based on Phylogenetic Information J. Peter Gogarten University of Connecticut Dept. of.

Summer 2008 Workshop in Biology and Multimedia for High School Teachers.

TAXONOMY Presentation made by: sakura023. Need to Classify.

Systematics The study of biological diversity in an evolutionary context.

Coalescence and the Cenancestor J. Peter Gogarten University of Connecticut Department of Molecular and Cell Biology.

Darwin’s Theory of Evolution

Chapter 26: Phylogeny and the Tree of Life Objectives 1.Identify how phylogenies show evolutionary relationships. 2.Phylogenies are inferred based homologies.

BINF6201/8201 Molecular phylogenetic methods

Bioinformatics 2011 Molecular Evolution Revised 29/12/06.

Underlying Principles of Zoology Laws of physics and chemistry apply. Principles of genetics and evolution important. What is learned from one animal group.

Modern Systematics Phylogenetics Phylogenetic tree Cladistics

Down with Creationism In the early 18 th century the commonly held belief of Creationism was being questioned Extinctions such as the dodo led them to.

26.1 Organisms Evolve Through Genetic Change Occurring Within Populations. “Nothing in Biology makes sense except in the light of Evolution” –Theodosius.

11.6 Patterns in Evolution Evolution through natural selection is not random.

Phylogeny & Systematics

Cenancestor (aka LUCA or MRCA) can be placed using the echo remaining from the early expansion of the genetic code. reflects only a single cellular component.

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?

Chapter 26 Phylogeny and Systematics. Tree of Life Phylogeny – evolutionary history of a species or group - draw information from fossil record - organisms.

Chapter 18 Phylogeny and the Tree of Life. Phylogeny u Phylon = tribe, geny = genesis or origin u The evolutionary history of a species or a group of.

Chapter 26 Phylogeny and the Tree of Life

Phylogeny and the Tree of Life

Comparative Genomics and New Evolutionary Biology

The Coral of Life (Darwin)

EVIDENCE OF EVOLUTION.

The Ribosomal “Tree of Life”

Evolution and Classification

Endeavour to reconstruct the characters of each hypothetical ancestor.

KEY CONCEPT Evolution occurs in patterns.

Why could a gene tree be different from the species tree?

The Ribosomal “Tree of Life”

Reading Phylogenetic Trees

Evolution and Classification Essential Question:

Frederick M. Cohan, Elizabeth B. Perry Current Biology

The Ribosomal “Tree of Life”

Phylogenetics Chapter 26.

KEY CONCEPT Evolution occurs in patterns.

Chapter 25 Essential Questions

KEY CONCEPT Evolution occurs in patterns.

PHYLOGENETIC TREES.

Chapter 26 Phylogeny and the Tree of Life

Chapter 20 Phylogeny and the Tree of Life

Phylogeny and the Tree of Life

Chapter 18: Evolution and Origin of Species

The Ribosomal “Tree of Life”

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

Evolution Biology Mrs. Johnson.

Presentation transcript:

Trees as a Tool to Visualize Evolutionary History Family trees (Charles Darwin http://www.aboutdarwin.com/) Lamarck’s “Tree of Life” (1815) Page B26 from Charles Darwin’s (1809-1882) notebook (1837) Lebensbaum from Ernst Haeckel, 1874 “The tree of life should perhaps be called the coral of life, base of branches dead” PHYLOGENY: from Greek phylon, race or class, and -geneia, born. “the origin and evolution of a set of organisms, usually of a species” (Wikipedia);

Small subunit ribosomal RNA (16S) based tree of life. Carl Woese, George Fox, and many others.

The Tree of Life according to SSU ribosomal RNA (+) strictly bifurcating no reticulation only extant lineages based on a single molecular phylogeny branch length is not proportional to time Eukaryotes Bacteria Archaea Cenancestor (aka MRCA or LUCA) as placed by ancient duplicated genes (ATPases, Signal recognition particles, EF) To Root

The Coral of Life (Darwin) The “Coral of Life” and the transfer of characters from now extinct into surviving lineages

Coalescence – the process of tracing lineages backwards in time to their common ancestors. Every two extant lineages coalesce to their most recent common ancestor. Eventually, all lineages coalesce to the cenancestor. t/2 (Kingman, 1982) Illustration is from J. Felsenstein, “Inferring Phylogenies”, Sinauer, 2003

EXTANT LINEAGES FOR THE SIMULATIONS OF 50 LINEAGES

Lineages Through Time Plot 10 simulations of organismal evolution assuming a constant number of species (200) throughout the simulation; 1 speciation and 1 extinction per time step. (green O) 25 gene histories simulated for each organismal history assuming 1 HGT per 10 speciation events (red x) log (number of surviving lineages) green: organismal lineages ; red: molecular lineages (with gene transfer)

The deviation from the “long branches at the base” pattern could be due to under sampling an actual radiation due to an invention that was not transferred following a mass extinction Bacterial 16SrRNA based phylogeny (from P. D. Schloss and J. Handelsman, Microbiology and Molecular Biology Reviews, December 2004.)