Advanced Biology

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Advanced Biology

• Chapter 18
• Classification

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Advanced BiologyChapter 18 Classification

• 18-1 History of Taxonomy
• 18-2 Modern Phylogenetic Taxonomy
• 18-3 Two Modern Systems of Classification

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18-1 History of Taxonomy

• What is Taxonomy?
• Early Systems of Classification
• Phylogeny

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Taxonomy

• The branch of biology that names and groups
  organisms according to their characteristics and
  evolutionary history.
• Classify the thousands of new species discovered
  each year.
• Biologists use the characteristics of newly
  discovered species to classify it with organisms
  having similar characteristics.
• The way we group organisms today continues to
  change and reflect the evolutionary history of
  organisms.

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Early Systems of Classification

• Aristotle
• Linnaeus

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Aristotle

• Greek Philosopher 384-322 BC
• First classified organisms more than 2000yrs ago
  as either plants or animals.
• Animals land dwellers, water dwellers, or air
  dwellers.
• Plants three categories based on differences in
  their stems.

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Aristotle
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Carolus Linnaeus

• Swedish naturalist (1707-1778)
• Devised a system of grouping organisms into
  hierarchical categories. Nested hierarchy.
• Used an organisms morphology (form and
  structure)

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Levels of Classification

• Kingdom
• Phylum or Division
• Class
• Order
• Family
• Genus
• Species

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Under the modern Linnaean system, the
classification of an organism places the organism
within a nested hierarchy of taxa. The hierarchy
ranges from the most general category (domain) to
the most specific (species).
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Binomial Nomenclature

• Scientific Name has two parts.
• 1st part is the genus
• 2nd part is the species which is the identifier
  or descriptive word.
• Genus name is capitalized and both names are
  underlined or written in italics.
• Latin used by all scientists as a standard.
• Linnaeus classified 1000s of organisms. Versions
  of his system are still used today.

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Scientific Names

• May describe the organism, suggest geographic
  range, or honor a person
• Homo sapiens (sapiens wise)
• Chaos chaos (amoeba never appear the same shape)
• Linnaea borealis (Linnaeus favorite, borealis
  northern)

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Seven-level System was arbitrary

• There is significant variation in some species to
  establish additional levels.

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Tomato varieties

• Botany a species may be split into subsets known
  as varieties. Example peaches and nectarines are
  both varieties of Prunis persica.

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• Zoology variations of a species that occur in
  different geographical areas. Example Terrapene
  Carolina triungui is a subspecies of the common
  eastern box turtle Terrapene Carolina that has 3
  rather than 4 toes on its hind foot.

Subspecies of rat snake
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Phylogeny

• Phylogeny is evolutionary history
• Much of Linnaeus work in classification is
  relevant even in the context of phylogeny because
  morphological features are largely influenced by
  genes and are clues of common ancestry.

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18-2 Modern Phylogenetic Taxonomy

• Systematics
• Cladistics

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Systematics

• The study of molecular biology created a wealth
  of information on organisms molecular nature and
  changed the nature of taxonomy.
• Taxonomists organize the tremendous diversity of
  living things in the context of evolution.

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Systematic Taxonomy

• Systematic Taxonomists use several lines of
  evidence to construct a phylogenetic tree.
• Modern taxonomic placement involves
• Morphology
• Chromosomal characteristics
• Nucleotide and amino acid sequences (chromosomes)
• Embryological development
• Information from the fossil record.

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Phylogenetic tree

• Family tree that shows the evolutionary
  relationships thought to exist among groups of
  organisms.
• Represents a hypothesis and is based on several
  lines of evidence.
• Subject to change as new information arises.
• Example Figure 18-3 p343

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Phylogenetic Tree
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Interpreting a Phylogenetic Tree

• Organism at base of tree is common ancestor to
  all the others in the tree.
• Branch points indicate the evolution of some
  characteristic that splits a group into two
  groups.
• Groups shown at tips of branches include
  organisms that have evolved most recently.

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The Fossil Record

• Provides clues to evolutionary relationships
• Some organisms such as some ocean invertebrates
  have fairly complete fossil records. Others are
  incomplete.
• May provide framework for phylogenetic tree which
  can then be confirmed with other lines of
  evidence.

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Fossil Record
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Fossil record (horse, whale)
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Morphology

• Homologous features
• Show decent from a common ancestor.
• Common basic structure. Example bird wings and
  bat wings.
• The greater the number of homologous features two
  organisms share, the more closely related they
  are thought to be.

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Homologous Features
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Homologous Features
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• Analogous features
• Evolved independently.
• Differ in structure. Example flys wings and
  bats wings.

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Analogous Features
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Embryological Patterns of Development

• Early patterns of embryological development
  provide evidence of phylogenetic relationships.
• Provide means of testing hypothesis about
  relationships that have been developed from other
  lines of evidence.
• Blastophore formation In echinoderms and
  chordates, indentation forms the posterior end of
  the digestive system, in other animals it forms
  the anterior end. Figure 18-4, p 344

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Embryonic Development
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Chromosomes and Macromolecules

• Taxonomists use comparisons of macromolecules
  such as DNA, RNA and proteins as a kind of
  molecular clock.
• Scientists compare amino acid sequences for
  homologous protein molecules of different
  species.
• The number of amino acid differences is a clue to
  how long ago two species diverged from a shared
  evolutionary ancestor.
• Not perfect because it assumes that all changes
  in amino acid sequencing are random and not
  affected by natural selection. Additionally amino
  acids can change at different rates in different
  organisms.

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Chromosomes and Macromolecules - continued

• Molecular clock model is used together with other
  data to estimate degrees of relatedness.
• Scientists also compare karyotypes or patterns of
  chromosomes of two related species.
• Regions of chromosomes that have the same pattern
  of banding are clues to the degree of relatedness.

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DNA comparisons (Artic bluegrass)
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DNA banding patterns
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This cladogram is based on similar amino acid
sequences in a specific protein produced by these
plants. The initials M,G, and so on indicate
different amino acids. The yellow squares
indicate differences within the
otherwise-identical sequences.
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This phylogenetic diagram is based on analyses of
the DNA of many kinds of mammals. These analyses
do not support a systematic grouping of pangolins
with either African aardvarks or South American
anteaters. Instead, pangolins seem to be most
closely related to carnivores, such as bears and
dogs. Biologists sometimes revise their
classifications in light of such new evidence.
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Cladistics

• Relatively new system of phylogenetic
  classification.
• Uses certain features of organisms called shared
  derived characteristics to establish evolutionary
  relationships.
• Derived character feature that apparently
  evolved only within the group under
  consideration. Example feathers in birds are
  inherited from a common ancestor.

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Cladograms

• Ancestral diagrams made by means of cladistic
  analysis. Figure 18-6 p346
• To interpret a cladogram
• Begin at the bottom and move up the axis that
  shows branch points.
• Groups and derived characteristics appeared in
  the order shown.
• Example all groups branching above hair have
  hair. Those below do not.

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Cladogram
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This cladogram groups several major kinds of
plants according to their shared, derived
characters. The most common character (vascular
tissue) is shared by all groups. The least common
character (flowers) separates flowering plants
from all other plants.
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Conflict between tradition taxonomy and newer
cladistics

• Traditional Snakes, lizards, crocodiles are all
  reptiles. Birds in class by themselves.
• Newer Dinosaurs are more closely related to
  birds and crocs than to snakes and lizards.
  Reptiles did not spring from one common ancestor
  but are a composite of several branches that have
  occurred during evolution of vertebrates.

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Traditional systematists placed crocodiles in the
class Reptilia, but placed birds in the class
Aves. In contrast, cladistic taxonomists have
grouped crocodiles and birds together in a clade
named Archosauria. Notice that clades do not have
category names such as class or phylum.
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18-3 Two Modern Systems of Classification

• Six Kingdom System
• Three Domain System

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Six Kingdom System

• Kingdom Archaebacteria
• Kingdom Eubacteria
• Kingdom Protists
• Kingdom Fungi
• Kingdom Plantae
• Kingdom Animalia

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Six Kingdoms
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Kingdom Archaebacteria
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Kingdom Archaebacteria

• Unicellular
• Prokaryotes with distinctive cell membranes
• Biochemical and genetic properties that differ
  from all other kinds of life.
• Some autotrophic produce food by chemosynthesis
  and methane waste.

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• Many live in harsh environments sulfurous hot
  springs, salty lakes, anaerobic environments,
  intestines of animals
• archae ancient
• May be directly descended from and very similar
  to first organisms on Earth

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Kingdom Eubacteria
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Kingdom Eubacteria

• eu true
• Unicellular, prokaryotes
• Bacteria that affect your life tooth decay, turn
  milk to yogurt, food poisoning, illness
• Most use oxygen, but a few cannot live in O2
• Both Eubacteria and archaebacteria make up the
  greatest number of living things on Earth.

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• Both Eubacteria and archaebacteria reproduce by
  binary fission but do have methods of genetic
  recombination to allow evolution to occur.
• Short generation times (as little as 30 minutes)
  allow rapid evolutionary response to
  environmental change. Example antibiotic
  resistant bacterial infection.

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Kingdom Protista
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Kingdom Protista

• Eukaryotic (membrane-bound true nucleus, linear
  chromosomes, membrane bound organelles)
• Mostly single-celled organisms, but some
  multicellular but lack specialized tissues
• Many species distantly related. Broad kingdom
  contains all eukaryotes that are not plants,
  animals, or fungi. 50,000 species.
• Sexual cycles of many are unknown but thought to
  have some process of genetic recombination.

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Kingdom Fungi
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Kingdom Fungi

• Heterotrophic
• Unicellular and multicellular
• Eukaryotic
• Absorb nutrients rather than ingesting them the
  way some protists such as amoebas do.
• Sexual cycles not known for many fungi. It is
  likely that all species have some way of
  promoting genetic recombination.
• 100,000 species mushrooms, puffballs, rusts,
  smuts, mildews, and molds.

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Kingdom Plantae
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Kingdom Plantae

• Multicellular plants
• All except for a few parasitic forms are
  autotrophic and use photosynthesis as a source of
  energy
• Eukaryotic
• Most live on land
• Most have a sexual cycle based on meiosis
• 350,000 species identified including mosses,
  ferns, conifers, flowering plants.

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Kingdom Animalia
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Kingdom Animalia

• Eukaryotic
• Multicellular
• Heterotrophs
• Most have symmetrical body organization and move
  about their environment
• Standard sexual cycle that employs meiosis for
  the recombination of genes.

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Three Domain System

• The young science of molecular biology has led to
  an alternative to the 6 kingdom system
• Carl Woese (1928- ) of University of Illinois.
  Comparing sequences of ribosomal RNA in many
  organisms. Estimated how long ago pairs of
  organisms shared a common ancestor.
• Phylogenetic tree drawn from this data shows that
  living things seem to fall naturally into 3 broad
  groups or domains. Figure 18-11 p350

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This phylogenetic diagram represents hypotheses
of the evolutionary relationships between the
major recognized groups of organisms. Notice the
alignment of the three domain names (Bacteria,
Archaea, and Eukarya) with three major branches
of the tree of life.
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The six-kingdom system of classification can be
aligned with the newer system of three domains.
However, biologists have proposed adding,
subdividing, or replacing some kingdoms.
Biologists have also proposed other levels of
taxa.
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The Three Domains

• Bacteria (Eubacteria)
• Archaea (Archaebacteria)
• Eukarya (Eukaryotes) includes Protista, Fungi,
  Plantae, Animalia

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Three Domains
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Three Domains
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Conclusions from the Three Domain System

• All eukaryotes have true nuclei with linear
  chromosomes and membrane-bound organelles.
• The most variation in Eukarya is among protists.
• When considered from the perspective of the
  complete diversity of life on Earth, the fungi,
  plants, and animals are quite similar to each
  other.

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