BIOLOGY 171

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BIOLOGY 171
CHAPTER 25 Phylogeny and Systematics
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Investigating the Tree of Life

• Phylogeny Evolutionary history of a species
• Systematics Study of the diversity and
  relationships of life.
• Molecular Systematics Use of DNA, RNA and other
  molecular evidence to infer evolutionary
  relationships between genes and genomes.

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HOW FOSSILS FORM

• Most fossils are formed in sedimentary rock.
• Most fossils result from preservation of hard
  rather than soft parts.
• Some fossils result from petrification

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HOW FOSSILS FORM

• TYPES OF FOSSILS
• Thin organic layers sandwiched between layers
  of rock.
• Molds and prints
• Trace fossils are footprints, burrows, etc.
• Entire organism is preserved.
• Anaerobic environments that prevent decay.
  (amber)

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AMBER
FOSSIL TYPES
MOLDS / PRINTS
HARD PARTS
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TRACE
FOSSIL TYPES
PETRIFICATION
ORGANIC LAYER
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LIMITATIONS OF THE FOSSIL RECORD

• All fossils are accidents of an unusual
  sequence of events.
• Many types of organisms or body parts are not
  easily fossilized.
• Only a small fraction of organisms to have
  lived produce fossils.
• An even smaller fraction of fossils are
  discovered.

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Morphological and Molecular Homologies

• Morphological homologies
• Molecular homologies
• Homology vs. Analogy
• Homoplasies
• Evaluating Molecular Homologies

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Evaluating Molecular Homologies
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MOLECULAR BIOLOGY AND SYSTEMATICS

• A. Protein Comparison
• B. DNA Comparison
• DNA-DNA Hybridization
• Restriction Mapping
• DNA Sequencing
• C. Analysis of Fossilized DNA
• D. Molecular Clocks

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CONVERGENT EVOLUTION
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CLASSIFICATION AN OVERVIEW

• EARLY HISTORY
• THEOPHRASTUS
• DE MATERIA MEDICA
• HERBALS - DOCTRINE OF SIGNATURE
• 17TH AND 18TH CENTURY - CLASSIFICATION
• CARLOLUS LINNAEUS
• BINOMIAL NOMENCLATURE
• Systema naturae
• GENUS AND SPECIFIC EPITHET

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TERMINOLOGY OF SYSTEMATICS

• Phylogeny
• Taxonomy
• Classification
• Taxon
• Hierarchy Of Classification
• DOMAIN, KINGDOM, DIVISION, CLASS, ORDER, FAMILY,
  GENUS, SPECIES
• Phylogenetic Trees

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Taxonomic Hierarchy
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Phylogenetic Systematics

• Cladogram Diagram illustrating patterns of
  shared characteristics. If shared
  characteristics are homologies then the cladogram
  forms the basis of a phylogenetic tree.
• Clade Ancestral species and all its
  descendants.
• Cladistics Pattern of systematics in which
  species are grouped into clades.

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CLADOGRAM
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Cladogram
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Cladistics

• A true clade is a group with a single common
  ancestor.
• Monophyletic single tribe/single common
  ancestor.
• Paraphyletic A grouping with a single common
  ancestor but not all descendents.
• Polyphyletic A grouping that lacks a single
  common ancestor.

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Cladistics
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Other Cladistic Factors

• Shared Primitive Character A characteristic
  that shared beyond the clade under study.
• Shared Derived Characteristic Evolutionary
  novelty unique to a particular clade.
• Ingroup Group of related species under study.
• Outgroup A species or group so species that are
  closely related to, but are outside the ingroup.

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Building a Cladogram
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Phylogenetic Trees and Timing

• Phylograms Length of branches reflect the
  number of changes that have occurred to a
  particular DNA sequence in that lineage.
• Ultrametric Trees The pattern is the same as a
  phylogram, but all branches traced to a common
  ancestor are the same length. Illustrates
  survival period for the lineage rather than the
  number of DNA changes.

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Phylograms and Ultrametric Trees
Phylograms
Ultrametric Trees
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Criteria for Construction of a Phylogenetic Tree

• Maximum Parsimony Based on the fewest
  evolutionary events to have occurred as shared
  derived characteristics.
• Parsimony Simplest explanation
• Occams Razor
• Maximum Likelihood With certain rules about DNA
  changes, over time a tree can be found that
  reflects the most likely sequence of evolutionary
  events.

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Maximum Parsimony
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Maximum Likelihood
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Genetic Factors for Change

• Phylogenetic Trees as Hypotheses
• Gene Duplication and Gene Families
• Orthologous Genes Homologous genes passed in a
  straight line.
• Paralogous Genes Duplicated genes found in more
  than copy in thesame genome.
• Genome Evolution

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Phylogenetic Hypotheses
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Orthologous and Paralogous Genes
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Tree of Life
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Molecular Clocks

• Based on measuring the absolute time of
  evolutionary change based on the observation that
  some genes or regions of the genome evolve at a
  constant rate.
• Neutral Theory
• Difficulties with Molecular Clocks

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FOSSIL DATING

• Relative Dating
• Sedimentation Rates
• Absolute Dating
• C-14 or U-238
• C-14 has a half-life of 5,600 years.
• The half-life of U-238 is 4.5 billion years.
• Racemization

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CARBON 14 DATING
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CARBON 14 DATING