Anatomy of a Cladistic Analysis
|
|
- Randolph Poole
- 6 years ago
- Views:
Transcription
1 Anatomy of a Cladistic Analysis Nico M. Franz School of Life Sciences, Arizona State University XXXI Willi Hennig Meeting UC Riverside June 26, 2012; Riverside, CA
2 From the abstract: "The monophyly of the Neotropical entimine weevil genus Exophthalmus Schoenherr, 1823 (Curculionidae: Entiminae: Eustylini Lacordaire) is reassessed." [ ] "The present study scrutinizes these traditional perspectives, based on a cladistic analysis of 143 adult morphological characters and 90 species, representing 30 genera and seven tribes of Neotropical entimine weevils." The character matrix yielded eight most-parsimonious cladograms (length = 239 steps; consistency index = 66; retention index = 91), with mixed clade support that remains particularly wanting for some of the deeper in-group divergences."
3 (A) E. agrestis (Boheman); (B) E. consobrinus (Marshall); (C) E. hieroglyphicus Chevrolat (D) E. impressus (Fabricius); (E) E. nicaraguensis Bovie; (F) E. quadrivittatus (Olivier) (G) E. quinquedecimpunctatus (Olivier); (H) E. roseipes (Chevrolat); (I) E. sulcicrus Champion (J) E. triangulifer Champion; (K) E. verecundus (Chevrolat); (L) E. vittatus (Linnaeus)
4 Fig. 2. Preferred cladogram & character state optimizations
5 Dissecting the process motivating themes "Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics." Franz Outline of an explanatory account of cladistic practice. Biol. Phil. 20:
6 Dissecting the process motivating themes "Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics." Franz Outline of an explanatory account of cladistic practice. Biol. Phil. 20: "The identification of the valid scope for character statements cannot be a matter of mere ostension, or rigid designation, but must be a matter of scientific theory construction. Scope expansion of character statements can result in a situation where purportedly similar structures, apparently denoted by the same name (proper name or kind name), are in fact not the same. The nonhomology of such characters may be revealed through morphological complexity at the comparative level, by tree topology at the analytical level, or both." Rieppel The performance of morphological characters in broad-scale phylogenetic analyses. Biol. J. Linn. Soc. 92:
7 Sneak preview: 60 matrices, 8 stages tracking the analysis
8 Legacy character assembly
9 Stage 1: legacy character assembly Lacordaire (1863) typically a 1-3 character system for tribes/genera. Source: Lacordaire Histoire naturelle des insectes, Vol. 6. Paris: Roret.
10 Stage 1: legacy character assembly Champion (1911) winged vs. wingless entimine groups Source: Champion Otiorhynchinae Alatae. In: Biologia Centrali-Americana, Vol. 4, Part 3. London.
11 Stage 1: legacy character assembly Character has a length of 10 steps in a narrowly scoped analysis (Exophthalmus and closely related genera).
12 van Emden (1944) state-of-the-art for entimine tribes / genera Source: van Emden A key to the genera of Brachyderinae of the world. Annals and Magazine of Natural History 11: ,
13 Anderson (2002) identifies subfamilies, genera; not tribes Source: Anderson Family 131. Curculionidae. In: Arnett et al. (Eds.): American Beetles, Vol. 2. Boca Raton, CRC Press; pp
14 Initial characters and states had a reputable pedigree
15 Initial characters and states had a reputable pedigree Lacordaire Histoire naturelle des insectes, Vol 6. Paris, Roret. Champion Otiorhynchinae Alatae. Biologia Centrali-Americana, Vol. 4, Part 3. London; pp van Emden A key to the genera of Brachyderinae of the world. Ann. Mag. Nat. Hist. 11: , Anderson Family 131. Curculionidae. In: American B, Vol. 2. Boca Raton, CRC Press; pp Franz Redescriptions of critical type species in the Eustylini Lacordaire (Coleoptera: Curculionidae: Entiminae). J. Nat. Hist. 44:
16 Early cladistic outcomes (Stage 1) 52 taxa
17 Early cladistic outcomes (Stage 1) 100 characters
18 Early cladistic outcomes (Stage 1) 547 steps! (~ 5.5 / char.)
19 Matrix 10 Select legacy characters
20 Consistency index and retention index rapid decline
21 Character coding binary, multi-state ~ 40% multi-state characters
22 Character provenance external, internal initially all external
23 Number of MPTs and nodes collapsed in consensus Return to initial homology assessments (chars./states). 3 trees, 3 collapsed Not publication worthy.
24 Rescoping starts
25 Examples of poorly performing characters ( recode / eliminate)
26 Matrix 18: Examples of deactivated characters
27 Matrices 11-17: rescoping phase I some examples
28 Intermediate stages 2-5 rescoping, taxon/character addition addressing poorest characters
29 Intermediate stages 2-5 rescoping, taxon/character addition evidence of large gaps in sampling
30 Intermediate stages 2-5 rescoping, taxon/character addition addition of out-/ingroup taxa (52 90)
31
32 Intermediate stages 2-5 rescoping, taxon/character addition new taxa new (unscoped) characters
33 Intermediate stages 2-5 rescoping, taxon/character addition rescoping all in expanded context
34 Consistency index and retention index steady increase
35 Character coding binary, multi-state > 90% binary characters "exploratory" reductive coding
36 Character provenance external, internal > 20% internal characters
37 Number of MPTs and nodes collapsed in consensus Focus on detail homology, perform "aggressive scope reduction" Still not ready for publication. > 1200 trees, > 35 collapsed
38 And so
39 Contingent rescoping tricarinate rostrum of Diaprepes spp. 7 species 17. "Rostrum tricarinate,
40 Contingent rescoping tricarinate rostrum of Diaprepes spp. Are these rostra also tricarinate (in homology to Diaprepes)? 7 species Exophthalmus Otiorhynchus Pachnaeus Phaops Rhinospathe 17. "Rostrum tricarinate,
41 Contingent rescoping tricarinate rostrum of Diaprepes spp. No, not if intermittent phylogenetic insights are transparently included. (1) present (0) absent ( ) inapplicable 7 species Exophthalmus Otiorhynchus (0) absent ( ) inapplicable ( ) inapplicable Pachnaeus Phaops Rhinospathe 17. "Rostrum tricarinate, with a characteristic combination of one median carina and two (dorso-) lateral, apically slightly diverging carinae, each carina narrow, moderately sharp."
42 Narrowly scoped, deep-level homologies
43 Narrowly scoped, deep-level homologies
44 Narrowly scoped, deep-level homologies
45 Terminal stages 6-8 added resolution, robustness narrowly rescoped characters, more stable tree length
46 Consistency index and retention index approaching "maximum" levels
47 Character coding binary, multi-state > 20% characters with inapplicables
48 Character provenance external, internal ~ 40% internal characters
49 Number of MPTs and nodes collapsed in consensus Ready for publication. 8 trees, 3 collapsed
50 Review from matrix 10 to 60 Topology, Optimization, Language
51 Overview of significant topology changes matrices 1-60 Transition of matrix yielded earliest "reliable" results.
52 Matrix 10 [topology] Exophthalmus spp. Nested within Exoph. 52 taxa 100 characters 4 MPTs L = 547 steps CI = 28 RI = 66 3 nodes collapsed Bremer support
53 Matrix 20 [topology] Exophthalmus spp. Nested within Exoph. 52 taxa (=) 69 characters ( 31) 3 MPTs ( 1) L = 159 steps ( 388) CI = 48 (+ 20) RI = 83 (+ 17) 3 nodes collapsed (=) Bremer support
54 Matrix 30 [topology] Exophthalmus spp. Nested within Exoph. 90 taxa (+ 38) 91 characters (+ 22) 2192 MPTs (+ 2189) L = 205 steps (+ 46) CI = 45 ( 3) RI = 83 (=) 38 nodes collapsed (+ 35) Bremer support
55 Matrix 60 [topology] Exophthalmus spp. Nested within Exoph. 90 taxa (=) 143 characters (+ 52) 8 MPTs ( 2184) L = 239 steps (+ 24) CI = 66 (+ 21) RI = 91 (+ 8) 3 nodes collapsed ( 35) Bremer support
56 Matrix 10 [optimization] 52 taxa 100 characters 4 MPTs L = 547 steps CI = 28 RI = 66 3 nodes collapsed Diagnoses unwieldy Synapomorphies rare Select legacy characters
57 Matrix 60 [optimization] 90 taxa (+ 38) 143 characters (+ 43) 8 MPTs (+ 4) L = 239 steps ( 308) CI = 66 (+ 38) RI = 91 (+ 25) 3 nodes collapsed (=) Diagnoses concise Synapomorph. common
58 Matrix 10 [language] Lacordaire Histoire naturelle des insectes, Vol 6. Paris, Roret. Champion Otiorhynchinae Alatae. Biologia Centrali-Americana, Vol. 4, Part 3. London; pp van Emden A key to the genera of Brachyderinae of the world. Ann. Mag. Nat. Hist. 11: , Anderson Family 131. Curculionidae. In: American B, Vol. 2. Boca Raton, CRC Press; pp Franz Redescriptions of critical type species in the Eustylini Lacordaire (Coleoptera: Curculionidae: Entiminae). J. Nat. Hist. 44:
59 Matrix 60 [language]
60 Related issue Which characters should constitute phenotype anatomy ontologies?
61 Related issue the value of parsimony-contingent homology Special emphasis on constructing phenotypic anatomy ontologies. "We have taken an integrative approach in the building of Uberon, and in doing so embrace multiple axes of classification. [ ] This homology-neutrality of Uberon is a deliberate design feature of the ontology. We believe that specifying homology relationships and descent from common ancestral structures is of obvious high value, but that this need not be tightly coupled to the development of an upper anatomical ontology." Mungall et al Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13: R5.
62 Related issue the value of parsimony-contingent homology Special emphasis on constructing phenotypic anatomy ontologies. "We have taken an integrative approach in the building of Uberon, and in doing so embrace multiple axes of classification. [ ] This homology-neutrality of Uberon is a deliberate design feature of the ontology. We believe that specifying homology relationships and descent from common ancestral structures is of obvious high value, but that this need not be tightly coupled to the development of an upper anatomical ontology." Mungall et al Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13: R5. "Explanatory homology hypotheses should not be mistaken and blended with morphological descriptions, which in their turn are by nature descriptive and not explanatory. [ ] Instead, we differentiate phylogenetic investigations into the step of producing data and the step of phylogenetic reasoning." Vogt et al The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 26:
63 So then is this what we have in mind for classes in phenotype ontologies? Source: Davis Delimiting baridine weevil evolution (Coleoptera: Curculionidae: Baridinae). Zool. J. Linn. Soc. 161:
64 Conclusions Analytical phylogenetic methods not only organize character information, but may furthermore have the purpose of shaping character individuation. In the case of the Exophthalmus analysis, I would have been hard pressed to arrive at the final descriptions of characters and states without benefitting from intermittent parsimony-driven inferences that led to the reweighting and rescoping of earlier homology assessments. It is not always conducive to a researcher's reputation to expose these practices, but they do and must occur frequently.
65 Conclusions Analytical phylogenetic methods not only organize character information, but may furthermore have the purpose of shaping character individuation. In the case of the Exophthalmus analysis, I would have been hard pressed to arrive at the final descriptions of characters and states without benefitting from intermittent parsimony-driven inferences that led to the reweighting and rescoping of earlier homology assessments. It is not always conducive to a researcher's reputation to expose these practices, but they do and must occur frequently. Under the cladistic paradigm, the most precise inferences of homology are often parsimony-influenced and parsimony-contingent, and the two notions are inextricably linked and entrenched in our maturing observational terminology. By integrating expressions of structural equivalence at increasingly greater scales, phenotype ontologies also run the risk of 'dialing down' the most precise and phylogenetically scoped assessments of homology that systematics can produce.
66 Acknowledgments WHS XXXI Organizers Juliana Cardona Duque, Jennifer Girón, Anyimilehidi Mazo Vargas, Quentin Wheeler NSF-DEB : "Systematics of eustyline and geonemine weevils: Connecting and contrasting Caribbean and Neotropical mainland radiations"
67
Anatomy of a cladistic analysis. Nico M. Franz*
Cladistics Cladistics () 9./cla. Anatomy of a cladistic analysis Nico M. Franz* School of Life Sciences, Arizona State University, PO Box 875, Tempe, AZ, 8587-5, USA Accepted May Abstract The sequential
More information(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise
Bot 421/521 PHYLOGENETIC ANALYSIS I. Origins A. Hennig 1950 (German edition) Phylogenetic Systematics 1966 B. Zimmerman (Germany, 1930 s) C. Wagner (Michigan, 1920-2000) II. Characters and character states
More informationReconstructing the history of lineages
Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics
More informationThe practice of naming and classifying organisms is called taxonomy.
Chapter 18 Key Idea: Biologists use taxonomic systems to organize their knowledge of organisms. These systems attempt to provide consistent ways to name and categorize organisms. The practice of naming
More informationLecture V Phylogeny and Systematics Dr. Kopeny
Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437
More informationHomework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics:
Homework Assignment, Evolutionary Systems Biology, Spring 2009. Homework Part I: Phylogenetics: Introduction. The objective of this assignment is to understand the basics of phylogenetic relationships
More information8/23/2014. 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 informationIntroduction to characters and parsimony analysis
Introduction to characters and parsimony analysis Genetic Relationships Genetic relationships exist between individuals within populations These include ancestordescendent relationships and more indirect
More informationHow 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 informationPhylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them?
Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies & cladograms? How do we read them? How do we estimate them? Carolus Linneaus:Systema Naturae (1735) Swedish botanist &
More information"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2011 University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2011 University of California, Berkeley B.D. Mishler March 31, 2011. Reticulation,"Phylogeography," and Population Biology:
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationIntegrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2012 University of California, Berkeley
Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2012 University of California, Berkeley B.D. Mishler April 12, 2012. Phylogenetic trees IX: Below the "species level;" phylogeography; dealing
More informationPHYLOGENY WHAT IS EVOLUTION? 1/22/2018. Change must occur in a population via allele
PHYLOGENY EXERCISE 1 AND 2 WHAT IS EVOLUTION? The theory that all living organisms on earth are related and have a common ancestor. These organism have changed over time and are continuing to change. Changes
More informationLecture 6 Phylogenetic Inference
Lecture 6 Phylogenetic Inference From Darwin s notebook in 1837 Charles Darwin Willi Hennig From The Origin in 1859 Cladistics Phylogenetic inference Willi Hennig, Cladistics 1. Clade, Monophyletic group,
More informationDr. 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 informationSystematics - BIO 615
A Knyght ther was, and that a worthy man, A Knyght ther was, and he was a worthy man, A Knyght ther was, and that a worthy man, A Knyght ther was, and he was a worthy man, A Knyght ther was, and he wasn
More informationEvaluating phylogenetic hypotheses
Evaluating phylogenetic hypotheses Methods for evaluating topologies Topological comparisons: e.g., parametric bootstrapping, constrained searches Methods for evaluating nodes Resampling techniques: bootstrapping,
More informationClassification, Phylogeny yand Evolutionary History
Classification, Phylogeny yand Evolutionary History 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
More informationUoN, 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 informationChapter 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"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley B.D. Mishler Jan. 22, 2009. Trees I. Summary of previous lecture: Hennigian
More informationOutline. 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--Therefore, congruence among all postulated homologies provides a test of any single character in question [the central epistemological advance].
Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler Jan. 29, 2008. The Hennig Principle: Homology, Synapomorphy, Rooting issues The fundamental
More informationNeed for systematics. Applications of systematics. Linnaeus plus Darwin. Approaches in systematics. Principles of cladistics
Topics Need for systematics Applications of systematics Linnaeus plus Darwin Approaches in systematics Principles of cladistics Systematics pp. 474-475. Systematics - Study of diversity and evolutionary
More informationChapter 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 informationMacroevolution 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 informationPhylogeny 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 informationESS 345 Ichthyology. Systematic Ichthyology Part II Not in Book
ESS 345 Ichthyology Systematic Ichthyology Part II Not in Book Thought for today: Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else,
More informationAmira 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 informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence
More informationNon-independence in Statistical Tests for Discrete Cross-species Data
J. theor. Biol. (1997) 188, 507514 Non-independence in Statistical Tests for Discrete Cross-species Data ALAN GRAFEN* AND MARK RIDLEY * St. John s College, Oxford OX1 3JP, and the Department of Zoology,
More informationC3020 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 informationName: 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 informationLecture 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 informationClassification 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 informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley. Parsimony & Likelihood [draft]
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2016 University of California, Berkeley K.W. Will Parsimony & Likelihood [draft] 1. Hennig and Parsimony: Hennig was not concerned with parsimony
More informationConsensus Methods. * You are only responsible for the first two
Consensus Trees * consensus trees reconcile clades from different trees * consensus is a conservative estimate of phylogeny that emphasizes points of agreement * philosophy: agreement among data sets is
More informationPOPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics
POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the
More informationPHYLOGENY & 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 informationClassification 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 informationThe Life System and Environmental & Evolutionary Biology II
The Life System and Environmental & Evolutionary Biology II EESC V2300y / ENVB W2002y Laboratory 1 (01/28/03) Systematics and Taxonomy 1 SYNOPSIS In this lab we will give an overview of the methodology
More informationAnatomy of a tree. clade is group of organisms with a shared ancestor. a monophyletic group shares a single common ancestor = tapirs-rhinos-horses
Anatomy of a tree outgroup: an early branching relative of the interest groups sister taxa: taxa derived from the same recent ancestor polytomy: >2 taxa emerge from a node Anatomy of a tree clade is group
More informationThe Tree of Life. Phylogeny
The Tree of Life Phylogeny Phylogenetics Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein sequences Each branch
More informationCHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny
CHAPTER 26 PHYLOGENY AND THE TREE OF LIFE Connecting Classification to Phylogeny To trace phylogeny or the evolutionary history of life, biologists use evidence from paleontology, molecular data, comparative
More informationOrganizing 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 informationAP 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 informationELE4120 Bioinformatics Tutorial 8
ELE4120 ioinformatics Tutorial 8 ontent lassifying Organisms Systematics and Speciation Taxonomy and phylogenetics Phenetics versus cladistics Phylogenetic trees iological classification Goal: To develop
More informationBiologists have used many approaches to estimating the evolutionary history of organisms and using that history to construct classifications.
Phylogenetic Inference Biologists have used many approaches to estimating the evolutionary history of organisms and using that history to construct classifications. Willi Hennig developed d the techniques
More informationIntegrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2012 University of California, Berkeley
Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2012 University of California, Berkeley B.D. Mishler Feb. 7, 2012. Morphological data IV -- ontogeny & structure of plants The last frontier
More informationChapter 10. Classification and Phylogeny of Animals. Order in Diversity. Hierarchy of taxa. Table Linnaeus introduced binomial nomenclature
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chapter 10 Classification and Phylogeny of Animals Order in Diversity History Systematic zoologists have three
More informationPhylogeny 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 informationX X (2) X Pr(X = x θ) (3)
Notes for 848 lecture 6: A ML basis for compatibility and parsimony Notation θ Θ (1) Θ is the space of all possible trees (and model parameters) θ is a point in the parameter space = a particular tree
More informationBiology 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 informationLab 06 Phylogenetics, part 1
Lab 06 Phylogenetics, part 1 phylogeny is a visual representation of a hypothesis about the relationships among a set of organisms. Phylogenetics is the study of phylogenies and and their development.
More informationPhylogeny 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 informationHow to read and make phylogenetic trees Zuzana Starostová
How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation
More informationChapter 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 informationPHYLOGENY 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 informationModern 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 informationTaxonomy. 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 informationFig. 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 informationarxiv: v1 [q-bio.pe] 6 Jun 2013
Hide and see: placing and finding an optimal tree for thousands of homoplasy-rich sequences Dietrich Radel 1, Andreas Sand 2,3, and Mie Steel 1, 1 Biomathematics Research Centre, University of Canterbury,
More informationWhat is Phylogenetics
What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)
More informationTaxonomy 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 informationHistorical Biogeography. Historical Biogeography. Systematics
Historical Biogeography I. Definitions II. Fossils: problems with fossil record why fossils are important III. Phylogeny IV. Phenetics VI. Phylogenetic Classification Disjunctions debunked: Examples VII.
More informationSurprise! A New Hominin Fossil Changes Almost Nothing!
Surprise! A New Hominin Fossil Changes Almost Nothing! Author: Andrew J Petto Table 1: Brief Comparison of Australopithecus with early Homo fossils Species Apes (outgroup) Thanks to Louise S Mead for comments
More informationIntegrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008
Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler March 18, 2008. Phylogenetic Trees I: Reconstruction; Models, Algorithms & Assumptions
More informationIntegrating Fossils into Phylogenies. Throughout the 20th century, the relationship between paleontology and evolutionary biology has been strained.
IB 200B Principals of Phylogenetic Systematics Spring 2011 Integrating Fossils into Phylogenies Throughout the 20th century, the relationship between paleontology and evolutionary biology has been strained.
More informationWorkshop: Biosystematics
Workshop: Biosystematics by Julian Lee (revised by D. Krempels) Biosystematics (sometimes called simply "systematics") is that biological sub-discipline that is concerned with the theory and practice of
More informationCLASSIFICATION OF LIVING THINGS. Chapter 18
CLASSIFICATION OF LIVING THINGS Chapter 18 How many species are there? About 1.8 million species have been given scientific names Nearly 2/3 of which are insects 99% of all known animal species are smaller
More informationESTIMATION OF CONSERVATISM OF CHARACTERS BY CONSTANCY WITHIN BIOLOGICAL POPULATIONS
ESTIMATION OF CONSERVATISM OF CHARACTERS BY CONSTANCY WITHIN BIOLOGICAL POPULATIONS JAMES S. FARRIS Museum of Zoology, The University of Michigan, Ann Arbor Accepted March 30, 1966 The concept of conservatism
More informationChapter 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 informationBiology 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 informationChapter 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 information1/27/2010. Systematics and Phylogenetics of the. An Introduction. Taxonomy and Systematics
Systematics and Phylogenetics of the Amphibia: An Introduction Taxonomy and Systematics Taxonomy, the science of describing biodiversity, mainly naming unnamed species, and arranging the diversity into
More informationChapter 22: Descent with Modification 1. BRIEFLY summarize the main points that Darwin made in The Origin of Species.
AP Biology Chapter Packet 7- Evolution Name Chapter 22: Descent with Modification 1. BRIEFLY summarize the main points that Darwin made in The Origin of Species. 2. Define the following terms: a. Natural
More informationCHAPTERS 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 informationUsing Trees for Classifications. Introduction
Using Trees for Classifications The Phylogenetic Cibele Caio Principles and Practice of Phylogenetic Systematics, Spring 2009 Introduction The impusle to characterize and classify species Ancient Aristoteles
More informationUnit 9: Evolution Guided Reading Questions (80 pts total)
Name: AP Biology Biology, Campbell and Reece, 7th Edition Adapted from chapter reading guides originally created by Lynn Miriello Unit 9: Evolution Guided Reading Questions (80 pts total) Chapter 22 Descent
More informationConcept 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 informationSystematics Lecture 3 Characters: Homology, Morphology
Systematics Lecture 3 Characters: Homology, Morphology I. Introduction Nearly all methods of phylogenetic analysis rely on characters as the source of data. A. Character variation is coded into a character-by-taxon
More informationPhylogenetics: Parsimony
1 Phylogenetics: Parsimony COMP 571 Luay Nakhleh, Rice University he Problem 2 Input: Multiple alignment of a set S of sequences Output: ree leaf-labeled with S Assumptions Characters are mutually independent
More informationIntroduction to Biosystematics - Zool 575
Introduction to Biosystematics Lecture - Outline. Four steps in Phylogenetic Inference 2. Data - Selection 3. - What is it? - How does one recognize it? 4.. haracter (data) selection (not too fast, not
More informationMicrobial 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 informationA (short) introduction to phylogenetics
A (short) introduction to phylogenetics Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR Statistics, Millport Field
More informationAlgorithms 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 informationOEB 181: Systematics. Catalog Number: 5459
OEB 181: Systematics Catalog Number: 5459 Tu & Th, 10-11:30 am, MCZ 202 Wednesdays, 2-4 pm, Science Center 418D Gonzalo Giribet (Biolabs 1119, ggiribet@oeb.harvard.edu) Charles Marshall (MCZ 111A, cmarshall@fas.harvard.edu
More informationPhylogenetic analyses. Kirsi Kostamo
Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,
More informationIntroduction to Biosystematics - Zool 575
Introduction to Biosystematics Lecture 10 - Introduction to Phylogenetics 1. Pre Lamarck, Pre Darwin Classification without phylogeny 2. Lamarck & Darwin to Hennig (et al.) Classification with phylogeny
More informationQuestions we can ask. Recall. Accuracy and Precision. Systematics - Bio 615. Outline
Outline 1. Mechanistic comparison with Parsimony - branch lengths & parameters 2. Performance comparison with Parsimony - Desirable attributes of a method - The Felsenstein and Farris zones - Heterotachous
More informationPhyletic groups on networks. Ward C. Wheeler*
Cladistics Cladistics 30 (2014) 447 451 10.1111/cla.12062 Phyletic groups on networks Ward C. Wheeler* Division of Invertebrate Zoology, American Museum of Natural History, Central Park West @ 79th Street,
More information9/19/2012. 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 informationSPECIATION. 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 informationThe Tree of Life. Chapter 17
The Tree of Life Chapter 17 1 17.1 Taxonomy The science of naming and classifying organisms 2000 years ago Aristotle Grouped plants and animals Based on structural similarities Greeks and Romans included
More informationBiology 2. Lecture Material. For. Macroevolution. Systematics
Biology 2 Macroevolution & Systematics 1 Biology 2 Lecture Material For Macroevolution & Systematics Biology 2 Macroevolution & Systematics 2 Microevolution: Biological Species: Two Patterns of Evolutionary
More informationA Phylogenetic Network Construction due to Constrained Recombination
A Phylogenetic Network Construction due to Constrained Recombination Mohd. Abdul Hai Zahid Research Scholar Research Supervisors: Dr. R.C. Joshi Dr. Ankush Mittal Department of Electronics and Computer
More informationGENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS.
!! www.clutchprep.com CONCEPT: OVERVIEW OF EVOLUTION Evolution is a process through which variation in individuals makes it more likely for them to survive and reproduce There are principles to the theory
More information