Nature Biotechnology: doi: /nbt Supplementary Figure 1. Detailed overview of the primer-free full-length SSU rrna library preparation.

Size: px
Start display at page:

Download "Nature Biotechnology: doi: /nbt Supplementary Figure 1. Detailed overview of the primer-free full-length SSU rrna library preparation."

Transcription

1 Supplementary Figure 1 Detailed overview of the primer-free full-length SSU rrna library preparation. Detailed overview of the primer-free full-length SSU rrna library preparation.

2 Supplementary Figure 2 Detailed overview of the primer-based full-length SSU rrna library preparation. Detailed overview of the primer-based full-length SSU rrna library preparation.

3 Supplementary Figure 3 rrna length distribution after adapter trimming. rrna length distribution after adapter trimming.

4 Supplementary Figure 4 Maximum-likelihood phylogenetic tree showing coverage of the domain Bacteria. Maximum-likelihood phylogenetic tree showing coverage of the domain Bacteria. The tree includes all bacterial OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1392 alignment positions, and the tree calculated using FastTree v SSE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. *Indicates clades that do not include a genome or pure culture reference sequence being based on classification of reference sequences in the Silva v. 128 taxonomy. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.

5 Supplementary Figure 5 Rarefaction curves for the different samples split based on kingdom. Rarefaction curves for the different samples split based on kingdom.

6 Supplementary Figure 6 Maximum-likelihood phylogenetic tree showing coverage of the domain Archaea. Maximum-likelihood phylogenetic tree showing coverage of the domain Archaea. The tree includes all archaeal OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1257 alignment positions, and the tree calculated using FastTree v S SE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. *Indicates clades that do not include a genome or pure culture reference sequence being based on classification of reference sequences in the Silva v taxonomy. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.

7 Supplementary Figure 7 Maximum-likelihood phylogenetic tree showing coverage of the domain Eukarya. Maximum-likelihood phylogenetic tree showing coverage of the domain Eukarya. The tree includes all eukaryotic OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1548 alignment positions, and the tree calculated using FastTree v S SE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.

8 Supplementary Figure 8 Error-correction of Oxford Nanopore MinION data using molecular tagging. Error-correction of Oxford Nanopore MinION data using molecular tagging. Error-rate of the individual error-corrected consensus sequences as a function of the number of reads used to generate the consensus sequence. 1 represents the raw 2D reads.

9

10 Supplementary Figure 9 Data processing overview. Data processing overview. An overview of the data processing steps, important data outputs and data types used for different analysis.

Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

More information

Robert Edgar. Independent scientist

Robert Edgar. Independent scientist Robert Edgar Independent scientist robert@drive5.com www.drive5.com "Bacterial taxonomy is a hornets nest that no one, really, wants to get into." Referee #1, UTAX paper Assume prokaryotic species meaningful

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

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Supplementary information S3 (box) Methods Methods Genome weighting The currently available collection of archaeal and bacterial genomes has a highly biased distribution of isolates across taxa. For example,

More information

Taxonomy and Clustering of SSU rrna Tags. Susan Huse Josephine Bay Paul Center August 5, 2013

Taxonomy and Clustering of SSU rrna Tags. Susan Huse Josephine Bay Paul Center August 5, 2013 Taxonomy and Clustering of SSU rrna Tags Susan Huse Josephine Bay Paul Center August 5, 2013 Primary Methods of Taxonomic Assignment Bayesian Kmer Matching RDP http://rdp.cme.msu.edu Wang, et al (2007)

More information

Microbiome: 16S rrna Sequencing 3/30/2018

Microbiome: 16S rrna Sequencing 3/30/2018 Microbiome: 16S rrna Sequencing 3/30/2018 Skills from Previous Lectures Central Dogma of Biology Lecture 3: Genetics and Genomics Lecture 4: Microarrays Lecture 12: ChIP-Seq Phylogenetics Lecture 13: Phylogenetics

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Supplementary information S1 (box). Supplementary Methods description. Prokaryotic Genome Database Archaeal and bacterial genome sequences were downloaded from the NCBI FTP site (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)

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

Exploring Microbes in the Sea. Alma Parada Postdoctoral Scholar Stanford University

Exploring Microbes in the Sea. Alma Parada Postdoctoral Scholar Stanford University Exploring Microbes in the Sea Alma Parada Postdoctoral Scholar Stanford University Cruising the ocean to get us some microbes It s all about the Microbe! Microbes = microorganisms an organism that requires

More information

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rrna Gene Based Diversity Studies

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rrna Gene Based Diversity Studies The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rrna Gene Based Diversity Studies Jonas Ghyselinck 1 *., Stefan Pfeiffer 2 *., Kim Heylen 1, Angela Sessitsch 2, Paul De Vos 1

More information

Chapter 17. Table of Contents. Objectives. Taxonomy. Classifying Organisms. Section 1 Biodiversity. Section 2 Systematics

Chapter 17. Table of Contents. Objectives. Taxonomy. Classifying Organisms. Section 1 Biodiversity. Section 2 Systematics Classification Table of Contents Objectives Relatebiodiversity to biological classification. Explainwhy naturalists replaced Aristotle s classification system. Identifythe main criterion that Linnaeus

More information

FIG S1: Rarefaction analysis of observed richness within Drosophila. All calculations were

FIG S1: Rarefaction analysis of observed richness within Drosophila. All calculations were Page 1 of 14 FIG S1: Rarefaction analysis of observed richness within Drosophila. All calculations were performed using mothur (2). OTUs were defined at the 3% divergence threshold using the average neighbor

More information

Amplicon Sequencing. Dr. Orla O Sullivan SIRG Research Fellow Teagasc

Amplicon Sequencing. Dr. Orla O Sullivan SIRG Research Fellow Teagasc Amplicon Sequencing Dr. Orla O Sullivan SIRG Research Fellow Teagasc What is Amplicon Sequencing? Sequencing of target genes (are regions of ) obtained by PCR using gene specific primers. Why do we do

More information

9.3 Classification. Lesson Objectives. Vocabulary. Introduction. Linnaean Classification

9.3 Classification. Lesson Objectives. Vocabulary. Introduction. Linnaean Classification 9.3 Classification Lesson Objectives Outline the Linnaean classification, and define binomial nomenclature. Describe phylogenetic classification, and explain how it differs from Linnaean classification.

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

An Automated Phylogenetic Tree-Based Small Subunit rrna Taxonomy and Alignment Pipeline (STAP)

An Automated Phylogenetic Tree-Based Small Subunit rrna Taxonomy and Alignment Pipeline (STAP) An Automated Phylogenetic Tree-Based Small Subunit rrna Taxonomy and Alignment Pipeline (STAP) Dongying Wu 1 *, Amber Hartman 1,6, Naomi Ward 4,5, Jonathan A. Eisen 1,2,3 1 UC Davis Genome Center, University

More information

Sec$on 9. Evolu$onary Rela$onships

Sec$on 9. Evolu$onary Rela$onships Sec$on 9 Evolu$onary Rela$onships Sec$on 9 Learning Goals Explain why the ribosomal 16S gene is a good marker for molecular phylogene$c comparisons. Be able to interpret a phylogene$c tree. Explain the

More information

Biology 2.1 Taxonomy: Domain, Kingdom, Phylum. ICan2Ed.com

Biology 2.1 Taxonomy: Domain, Kingdom, Phylum. ICan2Ed.com Biology 2.1 Taxonomy: Domain, Kingdom, Phylum ICan2Ed.com Taxonomy is the scientific field that catalogs, describes, and names living organisms. The way to divide living organisms into groups based on

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

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

Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae

Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae Frederik Schulz, Ilias Lagkouvardos, Florian Wascher, Karin Aistleitner, Rok Kostanjšek, Matthias Horn Supplementary

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

A. Incorrect! In the binomial naming convention the Kingdom is not part of the name.

A. Incorrect! In the binomial naming convention the Kingdom is not part of the name. Microbiology Problem Drill 08: Classification of Microorganisms No. 1 of 10 1. In the binomial system of naming which term is always written in lowercase? (A) Kingdom (B) Domain (C) Genus (D) Specific

More information

Taxonomy and Biodiversity

Taxonomy and Biodiversity Chapter 25/26 Taxonomy and Biodiversity Evolutionary biology The major goal of evolutionary biology is to reconstruct the history of life on earth Process: a- natural selection b- mechanisms that change

More information

Chapter 17. Organizing Life's Diversity

Chapter 17. Organizing Life's Diversity Chapter 17 Organizing Life's Diversity Key Concepts: Chapter 17 1. List the 3 domains and the 6 kingdoms. 2. Our current system of classification was originally based on structures; scientists now base

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

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

Taxonomical Classification using:

Taxonomical Classification using: Taxonomical Classification using: Extracting ecological signal from noise: introduction to tools for the analysis of NGS data from microbial communities Bergen, April 19-20 2012 INTRODUCTION Taxonomical

More information

Bergey s Manual Classification Scheme. Vertical inheritance and evolutionary mechanisms

Bergey s Manual Classification Scheme. Vertical inheritance and evolutionary mechanisms Bergey s Manual Classification Scheme Gram + Gram - No wall Funny wall Vertical inheritance and evolutionary mechanisms a b c d e * * a b c d e * a b c d e a b c d e * a b c d e Accumulation of neutral

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

Microbial Taxonomy and the Evolution of Diversity

Microbial Taxonomy and the Evolution of Diversity 19 Microbial Taxonomy and the Evolution of Diversity Copyright McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display. 1 Taxonomy Introduction to Microbial Taxonomy

More information

Honor pledge: I have neither given nor received unauthorized aid on this test. Name :

Honor pledge: I have neither given nor received unauthorized aid on this test. Name : Midterm Exam #1 MB 451 : Microbial Diversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : Date : Name : 1. What are the three primary evolutionary branches of

More information

Assigning Taxonomy to Marker Genes. Susan Huse Brown University August 7, 2014

Assigning Taxonomy to Marker Genes. Susan Huse Brown University August 7, 2014 Assigning Taxonomy to Marker Genes Susan Huse Brown University August 7, 2014 In a nutshell Taxonomy is assigned by comparing your DNA sequences against a database of DNA sequences from known taxa Marker

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

Assembly improvement: based on Ragout approach. student: Anna Lioznova scientific advisor: Son Pham

Assembly improvement: based on Ragout approach. student: Anna Lioznova scientific advisor: Son Pham Assembly improvement: based on Ragout approach student: Anna Lioznova scientific advisor: Son Pham Plan Ragout overview Datasets Assembly improvements Quality overlap graph paired-end reads Coverage Plan

More information

Other resources. Greengenes (bacterial) Silva (bacteria, archaeal and eukarya)

Other resources. Greengenes (bacterial)  Silva (bacteria, archaeal and eukarya) General QIIME resources http://qiime.org/ Blog (news, updates): http://qiime.wordpress.com/ Support/forum: https://groups.google.com/forum/#!forum/qiimeforum Citing QIIME: Caporaso, J.G. et al., QIIME

More information

Figure S1: Phylogenetic tree of Pseudomonas and related bacteria. Phylogenetic trees were generated using parsimony, neighbor-joining and maximum

Figure S1: Phylogenetic tree of Pseudomonas and related bacteria. Phylogenetic trees were generated using parsimony, neighbor-joining and maximum Figure S1: Phylogenetic tree of Pseudomonas and related bacteria. Phylogenetic trees were are indicated in bold. Sequences retrieved from Col du Midi (Alps) are designated by the word Coldumidi followed

More information

Bacillus anthracis. Last Lecture: 1. Introduction 2. History 3. Koch s Postulates. 1. Prokaryote vs. Eukaryote 2. Classifying prokaryotes

Bacillus anthracis. Last Lecture: 1. Introduction 2. History 3. Koch s Postulates. 1. Prokaryote vs. Eukaryote 2. Classifying prokaryotes Last Lecture: Bacillus anthracis 1. Introduction 2. History 3. Koch s Postulates Today s Lecture: 1. Prokaryote vs. Eukaryote 2. Classifying prokaryotes 3. Phylogenetics I. Basic Cell structure: (Fig.

More information

Supplementary Information

Supplementary Information The ISME Journal Supplementary Information Ciobanu et al. SI Tables Table S1 List of studied samples and depths Sample name Core depth below the seafloor (m) 1H3 4 2H1* 6 3H1* 15 3H5 21 4H1 25 4H5* 31

More information

concentration ( mol l -1 )

concentration ( mol l -1 ) concentration ( mol l -1 ) 8 10 0 20 40 60 80 100 120 140 160 180 methane sulfide ammonium oxygen sulfate (/10) b depth (m) 12 14 Supplementary Figure 1. Water column parameters from August 2011. Chemical

More information

Centrifuge: rapid and sensitive classification of metagenomic sequences

Centrifuge: rapid and sensitive classification of metagenomic sequences Centrifuge: rapid and sensitive classification of metagenomic sequences Daehwan Kim, Li Song, Florian P. Breitwieser, and Steven L. Salzberg Supplementary Material Supplementary Table 1 Supplementary Note

More information

Lecture 2 Carbon and Energy Transformations

Lecture 2 Carbon and Energy Transformations 1.018/7.30J Fall 2003 Fundamentals of Ecology Lecture 2 Carbon and Energy Transformations READINGS FOR NEXT LECTURE: Krebs Chapter 25: Ecosystem Metabolism I: Primary Productivity Luria. 1975. Overview

More information

Outline Classes of diversity measures. Species Divergence and the Measurement of Microbial Diversity. How do we describe and compare diversity?

Outline Classes of diversity measures. Species Divergence and the Measurement of Microbial Diversity. How do we describe and compare diversity? Species Divergence and the Measurement of Microbial Diversity Cathy Lozupone University of Colorado, Boulder. Washington University, St Louis. Outline Classes of diversity measures α vs β diversity Quantitative

More information

Fig. 26.7a. Biodiversity. 1. Course Outline Outcomes Instructors Text Grading. 2. Course Syllabus. Fig. 26.7b Table

Fig. 26.7a. Biodiversity. 1. Course Outline Outcomes Instructors Text Grading. 2. Course Syllabus. Fig. 26.7b Table Fig. 26.7a Biodiversity 1. Course Outline Outcomes Instructors Text Grading 2. Course Syllabus Fig. 26.7b Table 26.2-1 1 Table 26.2-2 Outline: Systematics and the Phylogenetic Revolution I. Naming and

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

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

Comparing Prokaryotic and Eukaryotic Cells

Comparing Prokaryotic and Eukaryotic Cells A prokaryotic cell Basic unit of living organisms is the cell; the smallest unit capable of life. Features found in all cells: Ribosomes Cell Membrane Genetic Material Cytoplasm ATP Energy External Stimuli

More information

SPECIES OF ARCHAEA ARE MORE CLOSELY RELATED TO EUKARYOTES THAN ARE SPECIES OF PROKARYOTES.

SPECIES OF ARCHAEA ARE MORE CLOSELY RELATED TO EUKARYOTES THAN ARE SPECIES OF PROKARYOTES. THE TERMS RUN AND TUMBLE ARE GENERALLY ASSOCIATED WITH A) cell wall fluidity. B) cell membrane structures. C) taxic movements of the cell. D) clustering properties of certain rod-shaped bacteria. A MAJOR

More information

Chapter 19. Microbial Taxonomy

Chapter 19. Microbial Taxonomy Chapter 19 Microbial Taxonomy 12-17-2008 Taxonomy science of biological classification consists of three separate but interrelated parts classification arrangement of organisms into groups (taxa; s.,taxon)

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

Probing diversity in a hidden world: applications of NGS in microbial ecology

Probing diversity in a hidden world: applications of NGS in microbial ecology Probing diversity in a hidden world: applications of NGS in microbial ecology Guus Roeselers TNO, Microbiology & Systems Biology Group Symposium on Next Generation Sequencing October 21, 2013 Royal Museum

More information

Ch 10. Classification of Microorganisms

Ch 10. Classification of Microorganisms Ch 10 Classification of Microorganisms Student Learning Outcomes Define taxonomy, taxon, and phylogeny. List the characteristics of the Bacteria, Archaea, and Eukarya domains. Differentiate among eukaryotic,

More information

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

Origins of Life. Fundamental Properties of Life. Conditions on Early Earth. Evolution of Cells. The Tree of Life

Origins of Life. Fundamental Properties of Life. Conditions on Early Earth. Evolution of Cells. The Tree of Life The Tree of Life Chapter 26 Origins of Life The Earth formed as a hot mass of molten rock about 4.5 billion years ago (BYA) -As it cooled, chemically-rich oceans were formed from water condensation Life

More information

Phylogeny and the Tree of Life

Phylogeny and the Tree of Life Chapter 26 Phylogeny and the Tree of Life Lecture Outline Overview: Investigating the Tree of Life Evolutionary biology is about both process and pattern. o The processes of evolution are natural selection

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

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

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

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

Genomic insights into the taxonomic status of the Bacillus cereus group. Laboratory of Marine Genetic Resources, Third Institute of Oceanography,

Genomic insights into the taxonomic status of the Bacillus cereus group. Laboratory of Marine Genetic Resources, Third Institute of Oceanography, 1 2 3 Genomic insights into the taxonomic status of the Bacillus cereus group Yang Liu 1, Qiliang Lai 1, Markus Göker 2, Jan P. Meier-Kolthoff 2, Meng Wang 3, Yamin Sun 3, Lei Wang 3 and Zongze Shao 1*

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

Chapter 1: Introduction: Themes in the Study of Life

Chapter 1: Introduction: Themes in the Study of Life Name Period Begin your study of biology this year by reading Chapter 1. It will serve as a reminder about biological concepts that you may have learned in an earlier course and give you an overview of

More information

Concept Modern Taxonomy reflects evolutionary history.

Concept Modern Taxonomy reflects evolutionary history. Concept 15.4 Modern Taxonomy reflects evolutionary history. What is Taxonomy: identification, naming, and classification of species. Common Names: can cause confusion - May refer to several species (ex.

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

Campbell Essential Biology, 4/e (Simon/Reece/Dickey)

Campbell Essential Biology, 4/e (Simon/Reece/Dickey) Campbell Essential Biology, 4/e (Simon/Reece/Dickey) Name MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Using the branching tree of life for

More information

Bioinformatics tools for phylogeny and visualization. Yanbin Yin

Bioinformatics tools for phylogeny and visualization. Yanbin Yin Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and

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

Chapter 18: Classification

Chapter 18: Classification Chapter 18: Classification Dichotomous Key A way to identify unknown organisms Contains major characteristics of groups of organisms Pairs of CONTRASTING descriptions 4. After each description key either

More information

something about srna in archaea

something about srna in archaea something about srna in archaea or: Processed Small RNAs in Archaea and BHB Elements Sarah Berkemer Bioinformatics Vienzig Archaea? Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 2 / 23

More information

Plants. SC.912.L.14.7 Relate the structure of each of the major plant organs and tissues to physiological processes.

Plants. SC.912.L.14.7 Relate the structure of each of the major plant organs and tissues to physiological processes. Plants SC.912.L.14.7 Relate the structure of each of the major plant organs and tissues to physiological processes. 1. Students will explain how the structures of plant tissues and organs are directly

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

Computational methods for predicting protein-protein interactions

Computational methods for predicting protein-protein interactions Computational methods for predicting protein-protein interactions Tomi Peltola T-61.6070 Special course in bioinformatics I 3.4.2008 Outline Biological background Protein-protein interactions Computational

More information

Phys 214. Planets and Life

Phys 214. Planets and Life Phys 214. Planets and Life Dr. Cristina Buzea Department of Physics Room 259 E-mail: cristi@physics.queensu.ca (Please use PHYS214 in e-mail subject) Lecture 16. Phylogenetic tree. Metabolism. Carbon and

More information

Prokaryote vs. Eukaryote

Prokaryote vs. Eukaryote DIVERSITY OF LIVING THINGS Prokaryote vs. Eukaryote 1. Test Monday 2. Lab Report Rough Draft (typed) due Wednesday 3. Lab Report Due Friday Oct 7th 4. Letter to MP due Tuesday Oct 11 th CAROLUS LINNAEUS

More information

Multiple Sequence Alignment. Sequences

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

More information

Bioinformatics Chapter 1. Introduction

Bioinformatics Chapter 1. Introduction Bioinformatics Chapter 1. Introduction Outline! Biological Data in Digital Symbol Sequences! Genomes Diversity, Size, and Structure! Proteins and Proteomes! On the Information Content of Biological Sequences!

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

Prokaryotes Bacteria And Archaea Study Guide Answers READ ONLINE

Prokaryotes Bacteria And Archaea Study Guide Answers READ ONLINE Prokaryotes Bacteria And Archaea Study Guide Answers READ ONLINE If you are searched for a ebook Prokaryotes bacteria and archaea study guide answers in pdf format, then you have come on to the correct

More information

Introduction to polyphasic taxonomy

Introduction to polyphasic taxonomy Introduction to polyphasic taxonomy Peter Vandamme EUROBILOFILMS - Third European Congress on Microbial Biofilms Ghent, Belgium, 9-12 September 2013 http://www.lm.ugent.be/ Content The observation of diversity:

More information

- conserved in Eukaryotes. - proteins in the cluster have identifiable conserved domains. - human gene should be included in the cluster.

- conserved in Eukaryotes. - proteins in the cluster have identifiable conserved domains. - human gene should be included in the cluster. NCBI BLAST Services DELTA-BLAST BLAST (http://blast.ncbi.nlm.nih.gov/), Basic Local Alignment Search tool, is a suite of programs for finding similarities between biological sequences. DELTA-BLAST is a

More information

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. Exam Name MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) In what way(s) is the science of biology influencing and changing our culture? A) by

More information

Supplementary Information

Supplementary Information Supplementary Information Supplementary Figure 1. Schematic pipeline for single-cell genome assembly, cleaning and annotation. a. The assembly process was optimized to account for multiple cells putatively

More information

Microbiology Helmut Pospiech

Microbiology Helmut Pospiech Microbiology http://researchmagazine.uga.edu/summer2002/bacteria.htm 05.04.2018 Helmut Pospiech The Species Concept in Microbiology No universally accepted concept of species for prokaryotes Current definition

More information

Classification of Living Things Test Review

Classification of Living Things Test Review Classification of Living Things Test Review #1 What is taxonomy? a. the scientific study of how living things are classified b. the name of Aristotle s classification system c. the process used by geologists

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

Database on the structure of large ribosomal subunit RNA

Database on the structure of large ribosomal subunit RNA 1997 Oxford University Press Nucleic Acids Research, 1997, Vol. 25, No. 1 117 122 Database on the structure of large ribosomal subunit RNA Peter De Rijk, Yves Van de Peer and Rupert De Wachter* Departement

More information

Building the Tree of Life

Building the Tree of Life 18.3 Building the Tree of Life Changing Ideas About Kingdoms This diagram shows some of the ways in which organisms have been classified into kingdoms since the 1700s. Three Domains Genetic analysis has

More information

Chapter 18 Systematics: Seeking Order Amidst Diversity

Chapter 18 Systematics: Seeking Order Amidst Diversity Chapter 18 Systematics: Seeking Order Amidst Diversity Bird Diversity in Indonesia Chapter 18 At a Glance 18.1 How Are Organisms Named and Classified? 18.2 What Are the Domains of Life? 18.1 How Are Organisms

More information

What is an archaeon and are the Archaea really unique?

What is an archaeon and are the Archaea really unique? 1 2 What is an archaeon and are the Archaea really unique? *For correspondence: ajith.harish@gmail.com 3 4 5 Ajith Harish 1* 1 Department of Cell and Molecular Biology, Structural and Molecular Biology

More information

Campbell Essential Biology, 5e (Simon/Yeh) Chapter 1 Introduction: Biology Today. Multiple-Choice Questions

Campbell Essential Biology, 5e (Simon/Yeh) Chapter 1 Introduction: Biology Today. Multiple-Choice Questions Campbell Essential Biology, 5e (Simon/Yeh) Chapter 1 Introduction: Biology Today Multiple-Choice Questions 1) In what way(s) is the science of biology influencing and changing our culture? A) by helping

More information

Vocabulary: Fill in the definition for each word. Use your book and/or class notes. You can put the words in your own words. Animalia: Archaea:

Vocabulary: Fill in the definition for each word. Use your book and/or class notes. You can put the words in your own words. Animalia: Archaea: Name: _ Due Date: _ Per: _ Unit 4.2 Study Guide Directions: Complete all sections to the best of your ability. On the day of the Quiz (the due date for this assignment) turn this in with all of your Unit

More information

Sequence Analysis, '18 -- lecture 9. Families and superfamilies. Sequence weights. Profiles. Logos. Building a representative model for a gene.

Sequence Analysis, '18 -- lecture 9. Families and superfamilies. Sequence weights. Profiles. Logos. Building a representative model for a gene. Sequence Analysis, '18 -- lecture 9 Families and superfamilies. Sequence weights. Profiles. Logos. Building a representative model for a gene. How can I represent thousands of homolog sequences in a compact

More information

K-means-based Feature Learning for Protein Sequence Classification

K-means-based Feature Learning for Protein Sequence Classification K-means-based Feature Learning for Protein Sequence Classification Paul Melman and Usman W. Roshan Department of Computer Science, NJIT Newark, NJ, 07102, USA pm462@njit.edu, usman.w.roshan@njit.edu Abstract

More information

Introduction to the SNP/ND concept - Phylogeny on WGS data

Introduction to the SNP/ND concept - Phylogeny on WGS data Introduction to the SNP/ND concept - Phylogeny on WGS data Johanne Ahrenfeldt PhD student Overview What is Phylogeny and what can it be used for Single Nucleotide Polymorphism (SNP) methods CSI Phylogeny

More information

Section 18-1 Finding Order in Diversity

Section 18-1 Finding Order in Diversity Name Class Date Section 18-1 Finding Order in Diversity (pages 447-450) Key Concepts How are living things organized for study? What is binomial nomenclature? What is Linnaeus s system of classification?

More information

Supplementary material to Whitney, K. D., B. Boussau, E. J. Baack, and T. Garland Jr. in press. Drift and genome complexity revisited. PLoS Genetics.

Supplementary material to Whitney, K. D., B. Boussau, E. J. Baack, and T. Garland Jr. in press. Drift and genome complexity revisited. PLoS Genetics. Supplementary material to Whitney, K. D., B. Boussau, E. J. Baack, and T. Garland Jr. in press. Drift and genome complexity revisited. PLoS Genetics. Tree topologies Two topologies were examined, one favoring

More information

Introduction to Evolutionary Concepts

Introduction to Evolutionary Concepts Introduction to Evolutionary Concepts and VMD/MultiSeq - Part I Zaida (Zan) Luthey-Schulten Dept. Chemistry, Beckman Institute, Biophysics, Institute of Genomics Biology, & Physics NIH Workshop 2009 VMD/MultiSeq

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

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