Biology 2

1
Taxonomy

• Biology 2
• Mr. Greene
• Unit 10

2
Bellringer

• Look through this chapter and list the name of
  each type of organism illustrated, such as
  cactuses, bees, humans, oaks, etc. Suggest
  reasons why a scientific method of clasification
  is useful to study these organisms.

3
Key Ideas

• Why do biologists have taxonomic systems?
• What makes up the scientific name of a species?
• What is the structure of the modern Linnaean
  system of classification?

4
Taxonomy

• the classification of organisms

5
The Need for Systems

• About 1.7 million species have been named and
  described by scientists.
• Scientists think that millions more are
  undiscovered.
• Biologists use taxonomic systems to organize
  their knowledge of organisms.
• These systems attempt to provide consistent ways
  to name and categorize organisms.
• Taxonomic systems do not use common names, which
  may be confusing because they are different in
  different places.

6
What's in a Scientific Name?

• scientific name - the two-word name each organism
  on Earth is assigned
• all biologists over the world use these names
• binomial nomenclature the system of assigning
  names
• genus 1st word describes organism in a
  general way
• group of organisms that share major  
  characteristics
• First letter is ALWAYS CAPITALIZED
• species 2nd word identifies the exact kind of
  living thing
• each different kind of organism
• ALWAYS LOWER CASE
• The correct name MUST include both parts of its
  scientific name

7
SCIENTIFIC NAMING RULES

• 1.  Must be Latin or constructed using Latin
  rules
• 2.  Two different organisms cannot be assigned
  the same name
• 3.  Organisms of the same genus must have
  different species names
• 4.  Organisms of different genera CAN have the
  same species name
• e.g.   green anole lizard     Anolis
  carolinensis
• chickadee                  Parus carolinensis
• 5.  Pick name that relates to organisms location,
  trait, etc.
• e.g.   Tyrannosaurus rex tyrant-lizard king

8
Why are names in Latin?

• Latin was used in academic circles in the Middle
  Ages when scientists began naming organisms.
• Hence, it was easier to communicate regardless of
  language barrier.
• Easier to keep names for all 1.7 million
  organisms in Latin then renaming them

9
Who Created the System?

• Carl Linnaeus - Swedish botanist
• long names were used before he came along
• (some up to 15 words long)
•              
• When reading or writing scientific names,
  remember the following
• if the genus/species is already given you can
  abbreviate the genus
• e.g.   Homo sapiens H. sapiens
• based on physical, genetic, biochemical and
  behavioral similarities
• taxon each level of the naming system

10
Biological Hierarchy of Classification
11
Taxanomic Hierarchy

• Kingdom            North America          
  Animalia
• Phylum               United States             
  Chordata
• Class                    Ohio                    
           Mammalia
• Order                  Lake                      
          Primates
• Family                 Mentor                    
       Hominidae
• Genus                 Center Street             
  Homo
• Species               6477                       
        Homo sapiens
•  
• Sam gave Fred one copper padlock key.
• King Philip came over from Geneva, Switzerland.

12
Classification of Ursus arctos
Coral snake
Abert squirrel
Sea star
Grizzly bear
Black bear
Giant panda
Red fox
KINGDOM Animalia
PHYLUM Chordata
CLASS Mammalia
ORDER Carnivora
FAMILY Ursidae
GENUS Ursus
SPECIES Ursus arctos
13
Classification of a Bee
14
Panthera leo? Part One
15
Panthera leo? Part Two
16
The Linnaean System

• The category domain has been invented since
  Linnaeus time.
• This category recognizes the most basic
  differences among cell types.
• All living things are now grouped into one of
  three domains.

17
The Linnaean System, continued

• A species is usually defined as a unique group of
  organisms united by heredity or interbreeding.
• In practice, scientists tend to define species
  based on unique features.
• For example, Homo sapiens is recognized as the
  only living primate species that walks upright
  and uses spoken language.

18
Summary

• Biologists use taxonomic systems to organize
  their knowledge of organisms. They attempt to
  provide consistent ways to name and categorize
  organisms.
• All scientific names for species are made up of
  two Latin or Latin-like terms.
• In the Linnaean system of classification,
  organisms are grouped at successive levels of a
  hierarchy based on similarities in their form and
  structure. The eight levels of modern
  classification are domain, kingdom, phylum,
  class, order, family, genus, and species.

19
Bellringer

• Write the names of as many different kinds of
  cats as you can think of. Most cats belong to the
  same genus, Felis. Identify which cats you think
  belong to the same species.

20
Key Ideas

• What problems arise when scientists try to group
  organisms by apparent similarities?
• Is the evolutionary past reflected in modern
  systematics?
• How is cladistics used to construct evolutionary
  relationships?
• What evidence do scientists use to analyze these
  relationships?

21
Traditional Systematics

• Scientists have traditionally used similarities
  in appearance and structure to group organisms.
  However, this approach has been problematic.
• Some groups look similar but turn out to be
  distantly related.
• Other groups look different but turn out to be
  closely related.

• For example, dinosaurs were once seen as a group
  of reptiles that became extinct millions of years
  ago.
• Birds were seen as a separate, modern group that
  was not related to any reptile group.
• Fossil evidence has convinced scientists that
  birds evolved from one of the many lineages of
  dinosaurs.
• Some scientists classify birds as a subgroup of
  dinosaurs.

22
Problems with Traditional Classification

• based on structure
• how would you classify dolphins?
• with fish because of aquatic life and limbs that
  look like fins
• with mammals because warm blooded and breathe air

23
Phylogenetics

• Scientists who study systematics are interested
  in phylogeny, or the ancestral relationships
  between species.
• Grouping organisms by similarity is often assumed
  to reflect phylogeny, but inferring phylogeny is
  complex in practice.
• Reconstructing a species phylogeny is like
  trying to draw a huge family tree over millions
  of generations.

• Not all similar characteristics are inherited
  from a common ancestor.
• Consider the wings of an insect and the wings of
  a bird.
• Both enable flight, but the structures of the two
  wings differ.
• Fossil evidence also shows that insects with
  wings existed long before birds appeared.

24
Phylogenetics, continued

• Through the process of convergent evolution,
  similarities may evolve in groups that are not
  closely related.
• Similar features may evolve because the groups
  have adopted similar habitats or lifestyles.
• Similarities that arise through convergent
  evolution are called analogous characters.

25
Phylogenetics, continued

• Grouping organisms by similarities is subjective.
• Some scientists may think one character is
  important, while another scientist does not.
• For example, systematists historically placed
  birds in a separate class from reptiles, giving
  importance to characters like feathers.

• Fossil evidence now shows that birds are
  considered part of the family tree of
  dinosaurs.
• This family tree, or phylogenetic tree,
  represents a hypothesis of the relationships
  between several groups.

26
Cladistics

• Cladistics is a method of analysis that infers
  phylogenies by careful comparisons of shared
  characteristics.
• Cladistics is an objective method that unites
  systematics with phylogenetics.
• Cladistic analysis is used to select the most
  likely phylogeny among a given set of organisms.

27
Cladistics, continued

• Cladistics focuses on finding characters that are
  shared between different groups because of shared
  ancestry.
• A shared character is defined as ancestral if it
  is thought to have evolved in a common ancestor
  of both groups.
• A derived character is one that evolved in one
  group but not the other.

28
Cladistics, continued

• For example, the production of seeds is a
  character that is present in all living conifers
  and flowering plants, and some prehistoric
  plants.
• Seed production is a shared ancestral character
  among those groups.
• The production of flowers is a derived character
  that is only shared by flowering plants.

29
Cladistics, continued

• Cladistics infers relatedness by identifying
  shared derived and ancestral characters among
  groups, while avoiding analogous characters.
• Scientists construct a cladogram to show
  relationships between groups.
• A cladogram is a phylogenetic tree that is drawn
  in a specific way.

30
Cladistics, continued

• Organisms are grouped together through
  identification of their shared derived
  characters.
• All groups that arise from one point on a
  cladogram belong to a clade.
• A clade is a set of groups that are related by
  descent from a single ancestral lineage.

31
Cladistics, continued

• Each clade is usually compared with an outgroup,
  or group that lacks some of the shared
  characteristics.
• The next slide shows a cladogram of different
  types of plants.
• Conifers and flowering plants form a clade.
• Ferns form the outgroup.

32
Cladogram Major Groups of Plants
33
Traditional Classification Versus Cladogram
Appendages
Conical Shells
Crustaceans
Gastropod
Crab
Crab
Limpet
Limpet
Barnacle
Barnacle
Molted exoskeleton
Segmentation
Tiny free-swimming larva
CLASSIFICATION BASED ON VISIBLE SIMILARITIES
CLADOGRAM
34
Traditional Classification Versus Cladogram
Appendages
Conical Shells
Crustaceans
Gastropod
Crab
Crab
Limpet
Limpet
Barnacle
Barnacle
Molted exoskeleton
Segmentation
Tiny free-swimming larva
CLASSIFICATION BASED ON VISIBLE SIMILARITIES
CLADOGRAM
35
Cladogram Major Groups of Plants
36
Inferring Evolutionary Relatedness, continued

• Morphological Evidence
• Morphology refers to the physical structure or
  anatomy of organisms.
• Large-scale morphological evidence, like seeds
  and flowers, have been well studied.
• Scientists must look carefully at similar traits,
  to avoid using analogous characters for
  classification.

37
Inferring Evolutionary Relatedness, continued

• An important part of morphology in multicellular
  species is the pattern of development from embryo
  to adult.
• Organisms that share ancestral genes often show
  similarities during the process of development.
• For example, the jaw of an adult develops from
  the same part of an embryo in every vertebrate
  species.

38
Inferring Evolutionary Relatedness, continued

• Molecular Evidence
• Scientists can now use genetic information to
  infer phylogenies.
• Recall that as genes are passed on from
  generation to generation, mutations occur.
• Some mutations may be passed on to all species
  that have a common ancestor.

39
Similarities in DNA and RNA

• often you cannot compare organisms that are
  diverse
• (i.e. elephants and an amoeba)
• all organisms use DNA and RNA to pass on info and
  to control growth and development
• DNA and RNA are a good way of comparing organisms
  
• humans a gene that codes for myosin (protein in
  muscles)
• yeast has same gene that codes for myosin that
  enables internal cell parts to move

40
Molecular Clocks

• models that use DNA comparisons to estimate then
  length of time that two species have been
  evolving independently
• i.e. pendulum clock
• it marks time with a swinging pendulum
• molecular clock
• marks time by mutations

41
Inferring Evolutionary Relatedness, continued

• Genetic sequence data are now used widely for
  cladistic analysis.
• First, the sequence of DNA bases in a gene (or of
  amino acids in a protein) is determined for
  several species.
• Then, each letter (or amino acid) at each
  position is compared.

42
Similarities in Amino Acid Sequences
43
Inferring Evolutionary Relatedness, continued

• At the level of genomes, alleles may be lost or
  added over time.
• Another form of molecular evidence is the
  presence or absence of specific allelesor the
  proteins that result from them.
• From this evidence, the relative timing between
  genetic changes can be inferred.

44
Inferring Evolutionary Relatedness, continued

• Evidence of Order and Time
• Cladistics can determine only the relative order
  of divergence, or branching, in a phylogenetic
  tree.
• The fossil record can often be used to infer the
  actual time when a group may have begun to
  branch off.
• For example, using cladistics, scientists have
  identified lancelets as the closest relative of
  vertebrates.

45
Inferring Evolutionary Relatedness, continued

• The oldest known fossils of vertebrates are about
  450 million years old.
• But the oldest lancelet fossils are 535 million
  years old.
• So, these two lineages must have diverged more
  than 535 million years ago.

46
Inferring Evolutionary Relatedness, continued

• DNA mutations occur at relatively constant rates,
  so they can be used as an approximate genetic
  clock.
• Scientists can measure the genetic differences
  between taxa and estimate time of divergence.

47
Inferring Evolutionary Relatedness, continued

• Inference Using Parsimony
• Modern systematists use the principle of
  parsimony to construct phylogenetic trees.
• This principle holds that the simplest
  explanation for something is the most reasonable,
  unless strong evidence exists against that
  explanation.
• Given two possible cladograms, the one that
  implies the fewest character changes between
  points is preferred.

48
Summary

• Scientists traditionally have used similarities
  in appearance and structure to group organisms.
  However, this approach has been problematic.
• Grouping organisms by similarity is often assumed
  to reflect phylogeny, but inferring phylogeny is
  complex in practice.

• Cladistic analysis is used to select the most
  likely phylogeny among a given set of organisms.
• Biologists compare many kinds of evidence and
  apply logic carefully in order to infer
  phylogenies.

49
Bellringer

• What are the six kingdoms representing life on
  Earth?

50
Key Ideas

• Have biologists always recognized the same
  kingdoms?
• What are the domains and kingdoms of the
  three-domain system of classification?

51
Updating Classification Systems

• For many years after Linnaeus created his system,
  scientists only recognized two kingdoms Plantae
  and Animalia.
• Biologists have added complexity and detail to
  classification systems as they have learned more.
• Many new taxa have been proposed, and some have
  been reclassified
• Sponges, for example, used to be classified as
  plants.
• Microscopes allowed scientists to study sponge
  cells.
• Scientists learned that sponge cells are much
  more like animal cells, so today sponges are
  classified as animals.

52
Updating Classification Systems, continued

• In the 1800s, scientists added Kingdom Protista
  as a taxon for unicellular organisms.
• Soon, they noticed differences between
  prokaryotic and eukaryotic cells.
• Scientists created Kingdom Monera for
  prokaryotes.

Plantae
Animalia
53
Updating Classification Systems, continued

• By the 1950s, Kingdoms Monera, Protista, Fungi,
  Plantae, and Animalia were used.
• In the 1990s, genetic data suggested two major
  groups of prokaryotes.
• Kingdom Monera was split into Kingdoms Eubacteria
  and Archaebacteria.

Monera
54
What Is a Species?

• basic unit of evolution
• gives rise to new genera, families, etc.
• new hierarchy results when enough changes have
  been made to species
• organisms that are able to interbreed to produce
  fertile offspring
• works for most animals
• horse and zebra have offspring that are sterile
• dogs, coyotes, wolves can interbreed and make a
  hybrid
• dogs different breeds is not the same thing as
  different species

55
Concept Map
Living Things
are characterized by
Important characteristics
which place them in
and differing
Domain Eukarya
Cell wall structures
such as
which is subdivided into
which place them in
which coincides with
which coincides with
56
The Three-Domain System

• As biologists saw differences between two kinds
  of prokaryotes, they saw similarities among
  eukaryotes.
• A new system divided all organisms into three
  domains Bacteria, Archaea, and Eukarya.
• Today, most biologists tentatively recognize
  three domains and six kingdoms.

57
Phylogenetic Diagram of Major Groups of Organisms
58
The Three-Domain System, continued

• Major taxa are defined by major characteristics,
  including
• Cell Type prokaryotic or eukaryotic
• Cell Walls absent or present
• Body Type unicellular or multicellular
• Nutrition autotroph (makes own food) or
  heterotroph (gets nutrients from other organisms)

59
The Three-Domain System, continued

• Related groups of organisms will also have
  similar genetic material and systems of genetic
  expression.
• Organisms may have a unique system of DNA, RNA,
  and proteins.
• The following slide shows major characteristics
  for organisms in each domain and kingdom.

60
Kingdom and Domain Characteristics
61

• 1/2) Monera
• evolved from a common
• unicellular
• ancestor 4 million years ago 
• lack nuclei
• lack organelles  
• oldest forms of life

62

• ARCHAE   
• A) Archaebacteria
• unicellular and prokaryotes and found in extreme
  environments
• gave rise to eukaryotes and evolved before oxygen
  filled atmosphere
• cell walls lack peptidoglycan
• extremophiles

63

• BACTERIA 
• B)  Eubacteria
• unicellular and prokaryotes with 5,000 species
• thick, rigid cell walls with peptidoglycan
• common environments
• gave rise to eukaryotic cell organelles
• both autotrophic and heterotrophic forms
• some require oxygen and some do not

64
The Three-Domain System

• Domain Eukarya is made up of Kingdoms Protista,
  Fungi, Plantae, and Animalia.
• Members of the domain are eukaryotes, which are
  organisms composed of eukaryotic cells.
• These cells have a complex inner structure that
  enabled cells to become larger than the earliest
  cells.

• This complex inner structure also enabled the
  evolution of multicellular organisms.
• All eukaryotes have cells with a nucleus and
  other internal compartments.
• Also, true multicellularity and sexual
  reproduction only occur in eukaryotes.

65

• EUKARYA
• 3)  Protist
• greatest variety
• some unicellular some are not
• some autotrophic some heterotrophic
• ancestors of plants, fungi, and animals
• includes protozoa (amoeba and paramecium) algae
  (kelp and seaweed)

66

• EUKARYA
• 4)  Fungi
• heterotrophic
• most are multicellular and feed on dead/decaying
  organic matter
• secrete digestive enzymes into food source
• they then absorb smaller food molecules into
  their bodies
• mushrooms, yeast (unicellular), molds
• thin filaments that penetrate the soil or
  decaying organisms
• 70,000 species

67

• EUKARYA
• 5)  Plant
• multicellular, photosynthetic autotrophs
• nonmotile (unable to move place to place)
• mosses, ferns, flowers, trees
• most grow on dry land, some grow in water
• have cell walls which contain cellulose
• green algae are their ancestors
• 350,000 species

68

• EUKARYA
• 6)  Animal
• multicellular and heterotrophic
• 1 million known species
• evolved in the ocean
• no cell walls
• nearly all have a nervous system of some sort
• 1 million species

69
Cladogram of Six Kingdoms and Three Domains
DOMAIN ARCHAEA
DOMAIN EUKARYA
Kingdoms
Eubacteria Archaebacteria Protista Plantae Fungi A
nimalia
DOMAIN BACTERIA
70
Summary

• Biologists have added complexity and detail to
  classification systems as they have learned more.
• Today, most biologists tentatively recognize
  three domains and six kingdoms.
• Domain Bacteria is equivalent to Kingdom
  Eubacteria.
• Domain Archaea is equivalent to Kingdom
  Archaebacteria.
• Domain Eukarya is made up of Kingdoms Protista,
  Fungi, Plantae, and Animalia.