Evolutionary Biology Concepts Molecular Evolution Phylogenetic Inference BIO520 BioinformaticsJim Lund Reading: Ch7.

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

Reading Phylogenetic Trees Gloria Rendon NCSA November, 2008.
Chapter 19 Evolutionary Genetics 18 and 20 April, 2004
Evidence of Evolution. Voyage of the Beagle Charles Darwin’s observations on a voyage around the world led to new ideas about species.
GENE TREES Abhita Chugh. Phylogenetic tree Evolutionary tree showing the relationship among various entities that are believed to have a common ancestor.
1 General Phylogenetics Points that will be covered in this presentation Tree TerminologyTree Terminology General Points About Phylogenetic TreesGeneral.
Classification of Living Things. 2 Taxonomy: Distinguishing Species Distinguishing species on the basis of structure can be difficult  Members of the.
Plant Molecular Systematics (Phylogenetics). Systematics classifies species based on similarity of traits and possible mechanisms of evolution, a change.
Summer Bioinformatics Workshop 2008 Comparative Genomics and Phylogenetics Chi-Cheng Lin, Ph.D., Professor Department of Computer Science Winona State.
Phylogenetic reconstruction
Molecular Evolution Revised 29/12/06
14 Molecular Evolution and Population Genetics
Phylogeny Reconstruction II. The edges of tree can be freely rotated without changing the relationships among the terminal nodes. Trees are like mobiles.
Evolution Test Study Guide Answers
Phylogenetic trees Sushmita Roy BMI/CS 576
TGCAAACTCAAACTCTTTTGTTGTTCTTACTGTATCATTGCCCAGAATAT TCTGCCTGTCTTTAGAGGCTAATACATTGATTAGTGAATTCCAATGGGCA GAATCGTGATGCATTAAAGAGATGCTAATATTTTCACTGCTCCTCAATTT.
Phylogenetic Analysis. 2 Introduction Intension –Using powerful algorithms to reconstruct the evolutionary history of all know organisms. Phylogenetic.
AP Bio Review Day 3 Agenda: 1.Phylogenetics and Evolution
Molecular phylogenetics
Population GENETICS.
Evolution: Lamarck Evolution: Change over time Evolution: Change over time Lamarck Lamarck Use / disuse Use / disuse Theory of inheritance of ACQUIRED.
Evolution. What is evolution? A basic definition of evolution… “…evolution can be precisely defined as any change in the frequency of alleles within a.
Speciation SJCHS. Evolution Microevolution: Change in a population ’ s gene pool from generation to generation Speciation: When one or more new species.
Chapter 24 Evolutionary Genetics © John Wiley & Sons, Inc.
TGCAAACTCAAACTCTTTTGTTGTTCTTACTGTATCATTGCCCAGAATAT TCTGCCTGTCTTTAGAGGCTAATACATTGATTAGTGAATTCCAATGGGCA GAATCGTGATGCATTAAAGAGATGCTAATATTTTCACTGCTCCTCAATTT.
Introduction to Phylogenetics
Unit 5 Evolution. Biological Evolution All of the changes that have transformed life on Earth from the earliest beginnings to the diversity of organisms.
26.1 Organisms Evolve Through Genetic Change Occurring Within Populations. “Nothing in Biology makes sense except in the light of Evolution” –Theodosius.
Phylogenetic Analysis Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics Figures from Higgs & Attwood.
Introduction to History of Life. Biological evolution consists of change in the hereditary characteristics of groups of organisms over the course of generations.
Chapter 16 Table of Contents Section 1 Genetic Equilibrium
Chapter 10 Phylogenetic Basics. Similarities and divergence between biological sequences are often represented by phylogenetic trees Phylogenetics is.
Phylogeny Ch. 7 & 8.
Phylogeny & the Tree of Life
Classification and Phylogenetic Relationships
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?
Mader: Biology 8 th Ed.. Population Genetics Genetic diversity in populations changes over generations Forces that cause populations to evolve Allele.
Biological Evolution Standard B – 5.4. Standard B-5 The student will demonstrate an understanding of biological evolution and the diversity of life. Indicator.
Evolution Review Standard B-5:The student will demonstrate an understanding of biological evolution and the diversity of life.
Chapter 26 Phylogeny and the Tree of Life
Evolution for Beginners. What is evolution? A basic definition of evolution… “…evolution can be precisely defined as any change in the frequency of alleles.
Lesson Overview Lesson Overview Modern Evolutionary Classification 18.2.
Standard B-5: The student will demonstrate an understanding of biological evolution and the diversity of life.
What is phylogenetic analysis and why should we perform it? Phylogenetic analysis has two major components: (1) Phylogeny inference or “tree building”
Tree Terminologies. Phylogenetic Tree - phylogenetic relationships are normally displayed in a tree-like diagram (phylogenetic tree/cladogram) - a cladogram.
Phylogeny and the Tree of Life
Evolution for Beginners
Phylogeny & the Tree of Life
5.4 Cladistics.
Cladistics (Ch. 22) Based on phylogenetics – an inferred reconstruction of evolutionary history.
Endeavour to reconstruct the characters of each hypothetical ancestor.
Modern Evolutionary Classification (Ch 18.2)
Warm-Up Contrast adaptive radiation vs. convergent evolution? Give an example of each. What is the correct sequence from the most comprehensive to least.
Warm-Up Contrast adaptive radiation vs. convergent evolution? Give an example of each. What is the correct sequence from the most comprehensive to least.
Phylogeny and Systematics
Reading Phylogenetic Trees
Evolutionary Biology Concepts
Warm-Up Contrast adaptive radiation vs. convergent evolution? Give an example of each. What is the correct sequence from the most comprehensive to least.
Phylogeny and Systematics (Part 6)
Evolution-Natural Selection
Chapter 26- Phylogeny and Systematics
Warm-Up Contrast adaptive radiation vs. convergent evolution? Give an example of each. What is the correct sequence from the most comprehensive to least.
Warm-Up Contrast adaptive radiation vs. convergent evolution? Give an example of each. What is the correct sequence from the most comprehensive to least.
Phylogenetic Trees Jasmin sutkovic.
Copyright Pearson Prentice Hall
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
1 2 Biology Warm Up Day 6 Turn phones in the baskets
Presentation transcript:

Evolutionary Biology Concepts Molecular Evolution Phylogenetic Inference BIO520 BioinformaticsJim Lund Reading: Ch7

Evolution Evolution is a process that results in heritable changes in a population spread over many generations. "In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed Worth Publishers, p.974

Levels of Evolution Changes in allele frequencies within a species. Speciation. Molecular changes: –Single bp changes. –Genomic changes (alterations in large DNA segments).

Branching Descent PopulationsIndividuals

Phylogeny Branching diagram showing the ancestral relations among species. “Tree of Life” History of evolutionary change FRAMEWORK for INFERENCE

The framework for phylogenetics How do we describe phylogenies? How do we infer phylogenies?

Inheritance DNA  RNA  Protein  Function

Ancestral Node or ROOT of the Tree Internal Nodes or Divergence Points (represent hypothetical ancestors of the taxa) Branches or Lineages Terminal Nodes A B C D E Represent the TAXA (genes, populations, species, etc.) used to infer the phylogeny Common Phylogenetic Tree Terminology

Phylogenetic trees diagram the evolutionary relationships between the taxa ((A,(B,C)),(D,E)) = The above phylogeny as nested parentheses Taxon A Taxon B Taxon C Taxon E Taxon D No meaning to the spacing between the taxa, or to the order in which they appear from top to bottom. This dimension either can have no scale (for ‘cladograms’), can be proportional to genetic distance or amount of change (for ‘phylograms’ or ‘additive’ trees). These say that B and C are more closely related to each other than either is to A, and that A, B, and C form a clade that is a sister group to the clade composed of D and E. If the tree has a time scale, then D and E are the most closely related.

Taxon A Taxon B Taxon C Taxon D genetic change Taxon A Taxon B Taxon C Taxon D no meaning Two types of trees Cladogram Phylogram or additive tree Meaning of branch length differs. All show the same evolutionary relationships, or branching orders, between the taxa.

Rooted vs Unrooted Trees

More Trees ABCDEF

Trees-3 ABCDEF

Extinction ABCDEF

Population Genetic Forces Natural Selection (fitness) Drift (homozygosity by chance) –much greater in small populations Mutation/Recombination (variation) Migration –homogenizes gene pools Hardy-Weinberg Paradigm p+q=1 p 2 + 2pq + q 2 =1

Modes of speciation Many ways speciation can occur, among the most common are: Geographic isolation. Reproductive isolation. –Sexual selection. –Behavioral isolation.

DNA, protein sequence change

Multiple Changes/No Change..CCU AUA GGG....CCC AUA GGG....CCC AUG GGG....CCC AUG GGC....CCU AUG GGC....CCU AUA GGC.. 5 mutations 1 DNA change 0 amino acid changes (net) Enumerating bp/aa changes underestimates evolutionary change

Mechanisms of DNA Sequence Change Neutral Drift vs Natural Selection Traditional selection model Neutral (Kimura/Jukes) Pan-neutralism

Rate of change (evolution) of hemoglobin protein Each point on the graph is for a pair of species, or groups of species. From Kimura (1983) by way of Evolution, Ridley, 3rd ed.

Mutation rate varies Gene-to-Gene

Rate varies Site-to-Site

From Evolution. Mark Rdley, 3rd Ed.

Constraints on “Silent” Changes Codon Biases-translation rates Transcription elongation rates –polymerase ‘pause’ sites “Silent” regulatory elements –select for or against presence/absence Overall genome structure

DNA, Protein Similarity Similarity by common descent –phylogenetic Similarity by convergence (rare) –functional importance Similarity by chance –random variation not limitless –particular problem in wide divergence

Homology-similar by common descent CCCAGG CCCAAG CCCAAA CCTAAA

Inferring Trees and Ancestors CCCAGG CCCAAG-> CCCAAG CCCAAA-> CCTAAA CCTAAA-> CCTAAC Not always straightforward. The data doesn’t always give a single, correct answer.

Homology, Orthology, Paralogy

Paralogy Trap

Improper Inference Garbage in, garbage out!

Our Goals Infer Phylogeny –Optimality criteria –Algorithm Phylogenetic inference –(interesting ones)

Watch Out “The danger of generating incorrect results is inherently greater in computational phylogenetics than in many other fields of science.” “…the limiting factor in phylogenetic analysis is not so much in the facility of software application as in the conceptual understanding of what the software is doing with the data.”