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

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

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

Transcription

1 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 molecular methods of classification can overcome many of the pitfalls associated with traditional methods. Molecular methods compare antibodies, DNA, RNA, or amino acid sequences to give insight to the relatedness of organisms. For example, evolutionary changes are indicated by substitutions in nucleotide and amino acid sequences. Possible even when no morphological, behavioral, or ecological links are present. Amino acid sequences Comparing amino acid sequences in a homologous protein can provide information about the relationships between different organisms. Hemoglobin was the first protein investigated. Structure includes a porphyrin (heme, that can reversibly bind to oxygen) attached to a globin polypeptide chain (>140 aa long). 1

2 Found in animals (hemoglobin-like molecules are also found in plants, fungi, and invertebrates). The conserved nature of this molecule implies an early place in evolution. In a normal, adult: Four polypeptide chains; two α and two β (α 2 β 2 ) In some adults: α 2 δ 2 Embryonic hemoglobin: α 2 γ 2 Myoglobin and ε chains of hemoglobin are present in some tissues. Differences in hemoglobin structures indicate two kinds of evolution. 1. Differing globin chains (α, β, γ, δ, ε) arose producing the variety carried by a particular organism. Why might differing structures of globin chains arise? Each were a variation of the same globin theme: 1. Chains are same length 2. Sequence similarity at many positions D structure similar similar function. 4. β, γ, and δ genes are closely linked on chromosome 11. What does this close linkage tell you about the evolution of hemoglobin? 2

3 2. Once produced, each globin chain followed its own evolutionary path. This lead to changes in its amino acid sequence in different species. 3

4 GENE DUPLICATION AND DIVERGENCE The differing globins likely did not evolve independently, and then accidentally converge in sequence and function. Question: How did differing molecules of such similar structure and function arise? Linkage studies suggest that gene duplication of an original globin-type gene took place. Once copies of the gene were present, each could theoretically undergo independent evolution leading to today s α, β, γ, δ, and ε chains. Question: How could you tell which one came first? And which one is the most recent? The temporal order of hemoglobin chain evolution can be deduced by comparing amino acid sequences. The greater the sequence difference, the longer the time to their common ancestor (and subsequently, the greater evolutionary distance). We know: The myoglobin chain differs most from the others (different amino acids at > 100 sites). α differs from β at 77 sites. β differs from γ at 39 sites but differs from δ at only 10 sites. Implies that: 1. The myoglobin gene formed from an early duplication. 2. A later duplication separated α and β genes. 3. β and δ represent the latest duplication

5 How do gene duplications arise? Unequal crossing over that results in increased chromosome material. Some duplicated genes have evolved completely different functions although they share common amino acid sequences. Amino acid sequence of α-lactalbumin protein is similar to that of lysozyme. Further evolutionary relationships include: products by ducts sugar is the substrate Once genes are duplicated, how long does it take for divergences to occur? Dependent on number of amino acid substitutions necessary to produce a differing function. However even one amino acid change can drive drastic changes. Example: A single amino acid substitution can convert lactate dehydrogenase (LDH) to malate dehydrogenase (MDH). LDH used in glycolysis (pyruvate lactate) MDH used in Krebs cycle (malate oxoloacetate) Change generated by a change from glutamine to arginine at the 102 nd polypeptide position. Is it ironic that this simple aa change drives a major functional alteration, but in two closely related cycles? 5

6 DETERMINING MOLECULAR PHYLOGENIES One can estimate the evolutionary similarity between two genes by determining the minimum number of mutations necessary to transform one amino acid in one sequence to another amino acid in the same position in the other sequence. Minimizing the number of mutations necessary to drive a given change is referred to as parsimony. Example: it is easier to explain that a phenylalanine codon (UUU) arose from a single nucleotide substitution in a serine codon (UCU UUU) than from a triple nucleotide substitution in a glutamic acid codon (GAA UUU). Once parsimoniously determined evolutionary distances between species are established, phylogenetic relationships can be resolved. Example: Assume the most parsimonious mutational distance between a protein in species A and B is 25, between A and C is 20, and between B and C is 30. Which two are most closely related? Assign legs x, y, and z to represent the numbers of mutations responsible for their divergence. 6

7 The phylogenetic relationship can be portrayed as follows: The length of the legs can be calculated: A B distance (25) is 5 mutations less than C B distance (30). Therefore, x is 5 mutations less than y. y + z = 30 -(x + z -= 25) y x = 5 Since y + x = 20 (A C distance) and y x = 5, we can determine y. y +x = 20 +(y - x = 5) 2y = 25 y = 12.5, and by substitution, x = 7.5 z = A B distance x = = 17.5, yielding: Estimated branch position 7

8 Using mutational data, we can generate phylogenetic trees that display relationships among varying organisms. Calculated with complex mathematical algorithms. Many trees are possible, but only one will represent the true phylogeny. How do we know when a tree is the best one? Bootstrapping calculates the proportion of acceptable trees in which a node appears when data is repeatedly sampled and replaced. Example: Resample sequences that feature sequence differences one hundred times to produce one-hundred trees. Some differences in the trees are omitted and some appear more than once over the course of the resamplings. Each sampling generates a tree in which a particular node (position) may or may not occur. The bootstrap value is the frequency (% of time) in which the same branch appears. NUCLEIC ACID PHYLOGENIES BASED ON DNA-DNA HYBRIDIZATIONS Homology among genes from different organisms can be calculated by measuring the degree to which homologous nucleotide sequences in single strands pair up to form double strands. Referred to as DNA reassociation. DNA is isolated from two organisms (X and Y) and dissociated into single strands, then allowed to reassociate into X-Y hybrid double strands. 8

9 The reassociation process can be monitored by noting the A 260 on a spectrophotometer. As the DNA reassociates (becomes double stranded) the A 260 will decrease. The rate of reassociation is proportional to the homology of DNA strands in the mixture. Method can be used to compare simple or complex mixtures of DNA comprising billions of nucleotides. DNA reassociation has been used to deduce the phylogenetic relationship of primates. 9

10 Note: paleontological evidence suggests that the lineages of Old World monkeys and apes-humans diverged 33 million years ago. A 7.7 o C change in the thermal stability of DNA from humans and Old World Monkeys has also been observed. This implies that every 1 o C shift in DNA thermal stability represents a 4.3 million year interval in the evolution of primates. DNA hybridization techniques have their detractors. Allows the placement of the bottom x-axis in Fig DNA hybridization compresses all divergence information into a single distance measurement. NUCLEIC ACID PHYLOGENIES BASED ON RESTRICTION ENZYME SITES Restriction enzymes recognize short (4 8), specific nucleotide sequences and cleave the DNA at these sites. Example: EcoRI recognizes the sequence: 5 GAATTC 3 3 CTTAAG 5 and will cut (restrict) the DNA between the G and A 10

11 Since the DNA from different species exhibits differing sequences, the placement of restriction sites will be species- (sometimes strain) specific. Therefore, each species DNA will have fragments of characteristic length following enzyme restriction. There are many restriction enzymes available with which DNA can be restricted. Therefore complex mixtures of DNA fragment lengths can be generated, each representative of a differing species = Restriction fragment length polymorphisms (RFLP) Restriction maps can allow a comparison between species. Example: mitochondrial DNA from humans and apes was restricted with 19 different enzymes. The enzymes cleaved the DNA at approximately 50 sites. Comparison of site placement can yield evolutionary data. 11

12 In agreement with previously determined phylogenies, humans share many more restriction sites with chimpanzees and gorillas than with orangutans and gibbons. However, branching is unclear. NUCLEIC ACID PHYLOGENIES BASED ON NUCLEOTIDE SEQUENCE COMPARISONS AND HOMOLOGIES The most accurate method for determining phylogenetic relationships between different organisms is the direct comparison of DNA sequences of the same (or homologous) gene. Databases archive volumes of sequence data. Genbank (NCBI) Sequence information has suggested several evolutionary events: 1. Extensive horizontal gene transfer between genomes. 2. Considerable amount of gene duplication 25% of the Bacillus subtilis genome 3. Many Archaea protein sequences are more similar to Bacteria than to eukaryotes. 12

13 4. Protein used in replication, transcription, and translation show greater similarity in Archaea and eukaryotes % of genes have no known function. 6. Roughly 480 genes might be the minimum required for life. Based on sequencing of Mycoplasma genitalium genome. Primary targets for sequencing analyses to determine phylogeny are the ribosomal RNA genes. The gold standard today is the 16S rrna gene (prokaryotes) and 18S rrna gene (eukaryotes), however Strickberger focuses on the 5S rrna gene. Why the rrnas? 1. Universally distributed in all organisms. Component of the protein synthesis machinery = similar function in different organisms 2. Gene features regions that are highly conserved as well as regions that are variable. Constant secondary structure. Allows for alignment and comparison of DNA sequences. RATES OF MOLECULAR CHANGE: EVOLUTIONARY CLOCKS Inherent in all phylogenies is that evolutionary differences arose due to mutational differences. The greater the number of differences, the greater the evolutionary distance between organisms. In Figure 12-11, the evolutionist used a time scale (1 o C of DNA thermal stability change reflected 4.3 million years of evolutionary time). In doing this, they have assumed that mutations occurred at a fixed rate over time. 13

14 Implies that an evolutionary clock determines the rate at which many mutations occur. Evidence can be found in the amino acid sequence of hemoglobin. Compare the α-hemoglobin amino acid sequence of several different organisms to that of sharks. How many differences are detected? Carp 85 Salamander 84 Chicken 83 Mouse 79 Human 79 Results show that although considerable morphological changes have occurred in the organisms, a constant rate of mutation must have occurred. The number of sequence differences in β-hemoglobin chains correlates with the time to a common ancestor for many organism pairs: Organism pair aa changes Time to common per 100 codons ancestor (million years) Human/monkey 5 30 Human/cattle Marsupial/placental mammal Bird/ mammal Shark/bony vertebrate If evolutionary clocks exist, then two consequences can be expected: 1. The lines of descent leading from a common ancestor to all contemporary descendents should have similar rates of fixed mutations. 2. The proportional rate of fixation that occurs in one gene relative to the rates of fixation in other genes stays the same throughout any line of descent. These expectation were tested: The amino acid sequences of seven proteins in 17 vertebrate taxa were examined. An evolutionary clock was calibrated using known and accepted dates of divergence. The temporal length of each line of descent was calculated 14

15 The number of nucleotide substitutions that occurred over a given length of time was compared among the 17 taxa. The results suggested that the rate at which the individual proteins changed varied significantly among the differing lines of descent. Indicated that molecular changes were not uniform for a specific protein or taxa. However, when nucleotide substitutions are averaged over all seven proteins for each branching point in the phylogeny, the rate of molecular change over time is constant. This procedure calibrates an evolutionary clock for these particular proteins and allows us to link change to time. The need to average the nucleotide substitutions among the different genes in order to achieve a linear relationship between time and nucleotide substitutions tells us that no one evolutionary clock applies to every nucleotide sequence. Why? Perhaps selection intensity fixes some mutations more securely than others. 15

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

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

Phylogenetic Trees. How do the changes in gene sequences allow us to reconstruct the evolutionary relationships between related species?

Phylogenetic Trees. How do the changes in gene sequences allow us to reconstruct the evolutionary relationships between related species? Why? Phylogenetic Trees How do the changes in gene sequences allow us to reconstruct the evolutionary relationships between related species? The saying Don t judge a book by its cover. could be applied

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

Bio 1B Lecture Outline (please print and bring along) Fall, 2007

Bio 1B Lecture Outline (please print and bring along) Fall, 2007 Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution

More information

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid.

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid. 1. A change that makes a polypeptide defective has been discovered in its amino acid sequence. The normal and defective amino acid sequences are shown below. Researchers are attempting to reproduce the

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

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

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

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

Genomes and Their Evolution

Genomes and Their Evolution Chapter 21 Genomes and Their Evolution 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

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

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

Organizing Life s Diversity

Organizing Life s Diversity 17 Organizing Life s Diversity section 2 Modern Classification Classification systems have changed over time as information has increased. What You ll Learn species concepts methods to reveal phylogeny

More information

Evidence for Evolution

Evidence for Evolution Evidence for Evolution 1. 2. 3. 4. 5. Paleontology Comparative Anatomy Embryology Comparative Biochemistry Geographical Distribution How old is everything? The History of Earth as a Clock Station 1: Paleontology

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

Microbial Taxonomy. Microbes usually have few distinguishing properties that relate them, so a hierarchical taxonomy mainly has not been possible.

Microbial Taxonomy. Microbes usually have few distinguishing properties that relate them, so a hierarchical taxonomy mainly has not been possible. Microbial Taxonomy Traditional taxonomy or the classification through identification and nomenclature of microbes, both "prokaryote" and eukaryote, has been in a mess we were stuck with it for traditional

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

SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology

SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of

More information

Name: Class: Date: ID: A

Name: Class: Date: ID: A Class: _ Date: _ Ch 17 Practice test 1. A segment of DNA that stores genetic information is called a(n) a. amino acid. b. gene. c. protein. d. intron. 2. In which of the following processes does change

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

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

Exploring Evolution & Bioinformatics

Exploring Evolution & Bioinformatics Chapter 6 Exploring Evolution & Bioinformatics Jane Goodall The human sequence (red) differs from the chimpanzee sequence (blue) in only one amino acid in a protein chain of 153 residues for myoglobin

More information

Microbes usually have few distinguishing properties that relate them, so a hierarchical taxonomy mainly has not been possible.

Microbes usually have few distinguishing properties that relate them, so a hierarchical taxonomy mainly has not been possible. Microbial Taxonomy Traditional taxonomy or the classification through identification and nomenclature of microbes, both "prokaryote" and eukaryote, has been in a mess we were stuck with it for traditional

More information

Microbial Taxonomy. Slowly evolving molecules (e.g., rrna) used for large-scale structure; "fast- clock" molecules for fine-structure.

Microbial Taxonomy. Slowly evolving molecules (e.g., rrna) used for large-scale structure; fast- clock molecules for fine-structure. Microbial Taxonomy Traditional taxonomy or the classification through identification and nomenclature of microbes, both "prokaryote" and eukaryote, has been in a mess we were stuck with it for traditional

More information

UNIT 5. Protein Synthesis 11/22/16

UNIT 5. Protein Synthesis 11/22/16 UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA

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

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

Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST

Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Introduction Bioinformatics is a powerful tool which can be used to determine evolutionary relationships and

More information

AP Biology Notes Outline Enduring Understanding 1.B. Big Idea 1: The process of evolution drives the diversity and unity of life.

AP Biology Notes Outline Enduring Understanding 1.B. Big Idea 1: The process of evolution drives the diversity and unity of life. AP Biology Notes Outline Enduring Understanding 1.B Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring Understanding 1.B: Organisms are linked by lines of descent from

More information

Big Idea 1: The process of evolution drives the diversity and unity of life. Sunday, August 28, 16

Big Idea 1: The process of evolution drives the diversity and unity of life. Sunday, August 28, 16 Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring understanding 1.B: Organisms are linked by lines of descent from common ancestry. Essential knowledge 1.B.1: Organisms

More information

Chapter 19 Organizing Information About Species: Taxonomy and Cladistics

Chapter 19 Organizing Information About Species: Taxonomy and Cladistics Chapter 19 Organizing Information About Species: Taxonomy and Cladistics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics

More information

Computational Biology: Basics & Interesting Problems

Computational Biology: Basics & Interesting Problems Computational Biology: Basics & Interesting Problems Summary Sources of information Biological concepts: structure & terminology Sequencing Gene finding Protein structure prediction Sources of information

More information

Biodiversity. The Road to the Six Kingdoms of Life

Biodiversity. The Road to the Six Kingdoms of Life Biodiversity The Road to the Six Kingdoms of Life How the 6 kingdoms came about At first, only two kingdoms were recognized Then Haeckel proposed a third kingdom Protista (where protists had both plant

More information

Chapters 25 and 26. Searching for Homology. Phylogeny

Chapters 25 and 26. Searching for Homology. Phylogeny Chapters 25 and 26 The Origin of Life as we know it. Phylogeny traces evolutionary history of taxa Systematics- analyzes relationships (modern and past) of organisms Figure 25.1 A gallery of fossils The

More information

Chapter 19: Taxonomy, Systematics, and Phylogeny

Chapter 19: Taxonomy, Systematics, and Phylogeny Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand

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

SPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together

SPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together SPECIATION Origin of new species=speciation -Process by which one species splits into two or more species, accounts for both the unity and diversity of life SPECIES BIOLOGICAL CONCEPT Population or groups

More information

Chapter 16: Reconstructing and Using Phylogenies

Chapter 16: Reconstructing and Using Phylogenies Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/

More information

"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

Outline. Classification of Living Things

Outline. Classification of Living Things Outline Classification of Living Things Chapter 20 Mader: Biology 8th Ed. Taxonomy Binomial System Species Identification Classification Categories Phylogenetic Trees Tracing Phylogeny Cladistic Systematics

More information

Unit 5: Taxonomy. KEY CONCEPT Organisms can be classified based on physical similarities.

Unit 5: Taxonomy. KEY CONCEPT Organisms can be classified based on physical similarities. KEY CONCEPT Organisms can be classified based on physical similarities. Linnaeus developed the scientific naming system still used today. Taxonomy is the science of naming and classifying organisms. White

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

Understanding relationship between homologous sequences

Understanding relationship between homologous sequences Molecular Evolution Molecular Evolution How and when were genes and proteins created? How old is a gene? How can we calculate the age of a gene? How did the gene evolve to the present form? What selective

More information

Molecular evolution. Joe Felsenstein. GENOME 453, Autumn Molecular evolution p.1/49

Molecular evolution. Joe Felsenstein. GENOME 453, Autumn Molecular evolution p.1/49 Molecular evolution Joe Felsenstein GENOME 453, utumn 2009 Molecular evolution p.1/49 data example for phylogeny inference Five DN sequences, for some gene in an imaginary group of species whose names

More information

Molecular Evolution & the Origin of Variation

Molecular Evolution & the Origin of Variation Molecular Evolution & the Origin of Variation What Is Molecular Evolution? Molecular evolution differs from phenotypic evolution in that mutations and genetic drift are much more important determinants

More information

Molecular Evolution & the Origin of Variation

Molecular Evolution & the Origin of Variation Molecular Evolution & the Origin of Variation What Is Molecular Evolution? Molecular evolution differs from phenotypic evolution in that mutations and genetic drift are much more important determinants

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

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p

Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p Organization of Genes Differs in Prokaryotic and Eukaryotic DNA Chapter 10 p.110-114 Arrangement of information in DNA----- requirements for RNA Common arrangement of protein-coding genes in prokaryotes=

More information

Warm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab

Warm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab Date: Agenda Warm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab Ask questions based on 5.1 and 5.2 Quiz on 5.1 and 5.2 How

More information

Biodiversity. The Road to the Six Kingdoms of Life

Biodiversity. The Road to the Six Kingdoms of Life Biodiversity The Road to the Six Kingdoms of Life How the 6 kingdoms came about At first, only two kingdoms were recognized Then Haeckel proposed a third kingdom Protista (where protists had both plant

More information

BIOLOGY 432 Midterm I - 30 April PART I. Multiple choice questions (3 points each, 42 points total). Single best answer.

BIOLOGY 432 Midterm I - 30 April PART I. Multiple choice questions (3 points each, 42 points total). Single best answer. BIOLOGY 432 Midterm I - 30 April 2012 Name PART I. Multiple choice questions (3 points each, 42 points total). Single best answer. 1. Over time even the most highly conserved gene sequence will fix mutations.

More information

MiGA: The Microbial Genome Atlas

MiGA: The Microbial Genome Atlas December 12 th 2017 MiGA: The Microbial Genome Atlas Jim Cole Center for Microbial Ecology Dept. of Plant, Soil & Microbial Sciences Michigan State University East Lansing, Michigan U.S.A. Where I m From

More information

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis Chapters 12&13 Notes: DNA, RNA & Protein Synthesis Name Period Words to Know: nucleotides, DNA, complementary base pairing, replication, genes, proteins, mrna, rrna, trna, transcription, translation, codon,

More information

Translation Part 2 of Protein Synthesis

Translation Part 2 of Protein Synthesis Translation Part 2 of Protein Synthesis IN: How is transcription like making a jello mold? (be specific) What process does this diagram represent? A. Mutation B. Replication C.Transcription D.Translation

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

BIOINFORMATICS LAB AP BIOLOGY

BIOINFORMATICS LAB AP BIOLOGY BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to

More information

Phylogeny & Systematics

Phylogeny & Systematics Phylogeny & Systematics Phylogeny & Systematics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics has revealed that despite

More information

Phylogeny and the Tree of Life

Phylogeny and the Tree of Life LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 26 Phylogeny and the Tree of Life

More information

Multiple Sequence Alignment. Sequences

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

More information

9/19/2012. Chapter 17 Organizing Life s Diversity. Early Systems of Classification

9/19/2012. Chapter 17 Organizing Life s Diversity. Early Systems of Classification Section 1: The History of Classification Section 2: Modern Classification Section 3: Domains and Kingdoms Click on a lesson name to select. Early Systems of Classification Biologists use a system of classification

More information

Protein Architecture V: Evolution, Function & Classification. Lecture 9: Amino acid use units. Caveat: collagen is a. Margaret A. Daugherty.

Protein Architecture V: Evolution, Function & Classification. Lecture 9: Amino acid use units. Caveat: collagen is a. Margaret A. Daugherty. Lecture 9: Protein Architecture V: Evolution, Function & Classification Margaret A. Daugherty Fall 2004 Amino acid use *Proteins don t use aa s equally; eg, most proteins not repeating units. Caveat: collagen

More information

Organizing Life on Earth

Organizing Life on Earth Organizing Life on Earth Inquire: Organizing Life on Earth Overview Scientists continually obtain new information that helps to understand the evolutionary history of life on Earth. Each group of organisms

More information

USING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES

USING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES USING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES HOW CAN BIOINFORMATICS BE USED AS A TOOL TO DETERMINE EVOLUTIONARY RELATIONSHPS AND TO BETTER UNDERSTAND PROTEIN HERITAGE?

More information

SECTION 17-1 REVIEW BIODIVERSITY. VOCABULARY REVIEW Distinguish between the terms in each of the following pairs of terms.

SECTION 17-1 REVIEW BIODIVERSITY. VOCABULARY REVIEW Distinguish between the terms in each of the following pairs of terms. SECTION 17-1 REVIEW BIODIVERSITY VOCABULARY REVIEW Distinguish between the terms in each of the following pairs of terms. 1. taxonomy, taxon 2. kingdom, species 3. phylum, division 4. species name, species

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 27: Evolutionary Genetics

Chapter 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 information

18.4 Embryonic development involves cell division, cell differentiation, and morphogenesis

18.4 Embryonic development involves cell division, cell differentiation, and morphogenesis 18.4 Embryonic development involves cell division, cell differentiation, and morphogenesis An organism arises from a fertilized egg cell as the result of three interrelated processes: cell division, cell

More information

Lecture 14 - Cells. Astronomy Winter Lecture 14 Cells: The Building Blocks of Life

Lecture 14 - Cells. Astronomy Winter Lecture 14 Cells: The Building Blocks of Life Lecture 14 Cells: The Building Blocks of Life Astronomy 141 Winter 2012 This lecture describes Cells, the basic structural units of all life on Earth. Basic components of cells: carbohydrates, lipids,

More information

Modern Evolutionary Classification. Section 18-2 pgs

Modern Evolutionary Classification. Section 18-2 pgs Modern Evolutionary Classification Section 18-2 pgs 451-455 Modern Evolutionary Classification In a sense, organisms determine who belongs to their species by choosing with whom they will mate. Taxonomic

More information

Emily Blanton Phylogeny Lab Report May 2009

Emily Blanton Phylogeny Lab Report May 2009 Introduction It is suggested through scientific research that all living organisms are connected- that we all share a common ancestor and that, through time, we have all evolved from the same starting

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

MACROEVOLUTION Student Packet SUMMARY EVOLUTION IS A CHANGE IN THE GENETIC MAKEUP OF A POPULATION OVER TIME Macroevolution refers to large-scale

MACROEVOLUTION Student Packet SUMMARY EVOLUTION IS A CHANGE IN THE GENETIC MAKEUP OF A POPULATION OVER TIME Macroevolution refers to large-scale MACROEVOLUTION Student Packet SUMMARY EVOLUTION IS A CHANGE IN THE GENETIC MAKEUP OF A POPULATION OVER TIME Macroevolution refers to large-scale evolutionary changes such as speciation events, origin of

More information

Biology 1B Evolution Lecture 2 (February 26, 2010) Natural Selection, Phylogenies

Biology 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 information

Chapter 17. From Gene to Protein. Biology Kevin Dees

Chapter 17. From Gene to Protein. Biology Kevin Dees Chapter 17 From Gene to Protein DNA The information molecule Sequences of bases is a code DNA organized in to chromosomes Chromosomes are organized into genes What do the genes actually say??? Reflecting

More information

Phylogeny 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 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 information

Introduction to Molecular and Cell Biology

Introduction to Molecular and Cell Biology Introduction to Molecular and Cell Biology Molecular biology seeks to understand the physical and chemical basis of life. and helps us answer the following? What is the molecular basis of disease? What

More information

Phylogeny and Systematics

Phylogeny and Systematics Chapter 25 Phylogeny and Systematics PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Modified by Maria Morlin racing phylogeny Phylogeny: he evolutionary

More information

Primate Diversity & Human Evolution (Outline)

Primate Diversity & Human Evolution (Outline) Primate Diversity & Human Evolution (Outline) 1. Source of evidence for evolutionary relatedness of organisms 2. Primates features and function 3. Classification of primates and representative species

More information

Bioinformatics Exercises

Bioinformatics Exercises Bioinformatics Exercises AP Biology Teachers Workshop Susan Cates, Ph.D. Evolution of Species Phylogenetic Trees show the relatedness of organisms Common Ancestor (Root of the tree) 1 Rooted vs. Unrooted

More information

GCD3033:Cell Biology. Transcription

GCD3033:Cell Biology. Transcription Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors

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

Microbiology / Active Lecture Questions Chapter 10 Classification of Microorganisms 1 Chapter 10 Classification of Microorganisms

Microbiology / Active Lecture Questions Chapter 10 Classification of Microorganisms 1 Chapter 10 Classification of Microorganisms 1 2 Bergey s Manual of Systematic Bacteriology differs from Bergey s Manual of Determinative Bacteriology in that the former a. groups bacteria into species. b. groups bacteria according to phylogenetic

More information

2012 Univ Aguilera Lecture. Introduction to Molecular and Cell Biology

2012 Univ Aguilera Lecture. Introduction to Molecular and Cell Biology 2012 Univ. 1301 Aguilera Lecture Introduction to Molecular and Cell Biology Molecular biology seeks to understand the physical and chemical basis of life. and helps us answer the following? What is the

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

1 ATGGGTCTC 2 ATGAGTCTC

1 ATGGGTCTC 2 ATGAGTCTC We need an optimality criterion to choose a best estimate (tree) Other optimality criteria used to choose a best estimate (tree) Parsimony: begins with the assumption that the simplest hypothesis that

More information

CREATING PHYLOGENETIC TREES FROM DNA SEQUENCES

CREATING PHYLOGENETIC TREES FROM DNA SEQUENCES INTRODUCTION CREATING PHYLOGENETIC TREES FROM DNA SEQUENCES This worksheet complements the Click and Learn developed in conjunction with the 2011 Holiday Lectures on Science, Bones, Stones, and Genes:

More information

Gene Families part 2. Review: Gene Families /727 Lecture 8. Protein family. (Multi)gene family

Gene Families part 2. Review: Gene Families /727 Lecture 8. Protein family. (Multi)gene family Review: Gene Families Gene Families part 2 03 327/727 Lecture 8 What is a Case study: ian globin genes Gene trees and how they differ from species trees Homology, orthology, and paralogy Last tuesday 1

More information

Taxonomy. Content. How to determine & classify a species. Phylogeny and evolution

Taxonomy. Content. How to determine & classify a species. Phylogeny and evolution Taxonomy Content Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Phylogeny and evolution Why Taxonomy? Classification Arrangement in groups or taxa (taxon = group) Nomenclature

More information

08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega

08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments

More information

BINF6201/8201. Molecular phylogenetic methods

BINF6201/8201. 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 information

Homeotic Genes and Body Patterns

Homeotic Genes and Body Patterns Homeotic Genes and Body Patterns Every organism has a unique body pattern. Although specialized body structures, such as arms and legs, may be similar in makeup (both are made of muscle and bone), their

More information

Quiz answers. Allele. BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA)

Quiz answers. Allele. BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA) BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 17: The Quiz (and back to Eukaryotic DNA) http://compbio.uchsc.edu/hunter/bio5099 Larry.Hunter@uchsc.edu Quiz answers Kinase: An enzyme

More information

Chapter 19. History of Life on Earth

Chapter 19. History of Life on Earth Chapter 19 History of Life on Earth Adapted from Holt Biology 2008 Chapter 19 Section 3: Evolution of Life Key Vocabulary Terms Adapted from Holt Biology 2008 Cyanobacteria Photosynthetic prokaryotes Adapted

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

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

The Theory of Evolution

The Theory of Evolution The Theory of Evolution Matthew Ferry Evolution The process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the Earth.

More information

Evolutionary Patterns, Rates, and Trends

Evolutionary Patterns, Rates, and Trends Evolutionary Patterns, Rates, and Trends Macroevolution Major patterns and trends among lineages Rates of change in geologic time Comparative Morphology Comparing body forms and structures of major lineages

More information

What is the central dogma of biology?

What is the central dogma of biology? Bellringer What is the central dogma of biology? A. RNA DNA Protein B. DNA Protein Gene C. DNA Gene RNA D. DNA RNA Protein Review of DNA processes Replication (7.1) Transcription(7.2) Translation(7.3)

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