Classification

1
Classification

• Each person might divide these shells into
  different categories
• Scientists often group and name, or classify,
  organisms using certain guidelines
• This makes it easier to discuss the types and
  characteristics of living things

2
Classification
3
Finding Order in Diversity

• For more than 3.5 billion years, life on Earth
  has been constantly changing
• Natural selection and other processes have led to
  a staggering diversity of organisms
• A tropical rain forest, for example, may support
  thousands of species per acre
• Recall that a species is a population of
  organisms that share similar characteristics and
  can breed with one another and produce fertile
  offspring
• Biologists have identified and named about 1.5
  million species so far
• They estimate that anywhere between 2 and 100
  million additional species have yet to be
  discovered

4
Why Classify?

• To study this great diversity of organisms,
  biologists must give each organism a name
• Biologists must also attempt to organize living
  things into groups that have biological meaning
• To study the diversity of life, biologists use a
  classification system to name organisms and group
  them in a logical manner

5
Why Classify?

• In the discipline known as taxonomy, scientists
  classify organisms and assign each organism a
  universally accepted name
• By using a scientific name, biologists can be
  certain that everyone is discussing the same
  organism
• When taxonomists classify organisms, they
  organize them into groups that have biological
  significance
• When you hear the word bird, for example, you
  immediately form a mental picture of the organism
  being discusseda flying animal that has feathers
• But science often requires smaller categories as
  well as larger, more general categories
• In a good system of classification, organisms
  placed into a particular group are more similar
  to each other than they are to organisms in other
  groups

6
Why Classify?

• You use classification systems also, for example,
  when you refer to teachers or mechanics, or
  more specifically, biology teachers or auto
  mechanics
• Such a process, like scientific classification,
  uses accepted names and common criteria to group
  things

7
Assigning Scientific Names

• By the eighteenth century, European scientists
  recognized that referring to organisms by common
  names was confusing
• Common names vary among languages and even among
  regions within a single country
• For example, a cougar can also be called a puma,
  a panther, or a mountain lion
• Furthermore, different species sometimes share a
  single common name
• In the United Kingdom, the word buzzard refers to
  a hawk, whereas in many parts of the United
  States, buzzard refers to a vulture
• To eliminate such confusion, scientists agreed to
  use a single name for each species
• Because eighteenth-century scientists understood
  Latin and Greek, they used those languages for
  scientific names
• This practice is still followed today in naming
  newly discovered species

8
Early Efforts at Naming Organisms 

• The first attempts at standard scientific names
  often described the physical characteristics of a
  species in great detail
• As a result, these names could be twenty words
  long!
• For example, the English translation of the
  scientific name of a particular tree might be
  Oak with deeply divided leaves that have no
  hairs on their undersides and no teeth around
  their edges
• This system of naming had another major drawback
• It was difficult to standardize the names of
  organisms because different scientists described
  different characteristics

9
Binomial Nomenclature 

• A major step was taken by Carolus Linnaeus, a
  Swedish botanist who lived during the eighteenth
  century
• He developed a two-word naming system called
  binomial nomenclature
• This system is still in use today
• In binomial nomenclature, each species is
  assigned a two-part scientific name
• The scientific name is always written in italics
• The first word is capitalized, and the second
  word is lowercased

10
Binomial Nomenclature 

• For example, the grizzly bear is called Ursus
  arctos
• The first part of the scientific namein this
  case, Ursusis the genus to which the organism
  belongs
• A genus (plural genera) is a group of closely
  related species
• The genus Ursus contains five other kinds of
  bears, including Ursus maritimus, the polar bear

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Binomial Nomenclature 

• The second part of a scientific namein this
  case, arctos or maritimusis unique to each
  species within the genus
• Often, this part of the name is a Latinized
  description of some important trait of the
  organism or an indication of where the organism
  lives
• The Latin word maritimus, referring to the sea,
  comes from the fact that polar bears often live
  on pack ice that floats in the sea

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Linnaeus's System of Classification

• Linnaeus's classification system is hierarchical
  that is, it consists of levels
• Linnaeus's hierarchical system of classification
  includes seven levels
• They arefrom smallest to largestspecies, genus,
  family, order, class, phylum, and kingdom
• In taxonomic nomenclature, or naming system, each
  of those levels is called a taxon (plural taxa),
  or taxonomic category

13
CLASSIFICATION

• Taxonomy is the science of grouping organisms
  according to their presumed natural relationship
• Common names add cause confusion to the
  classification system
• System used today is binomial nomenclature (two
  names)
• Developed by Linnaeus
• Placed structurally similar organisms into a
  group called a species
• Similar species into a larger group called a
  genus
• Similar genera into a family
• Similar families were placed into an order
• Similar orders in a class
• Similar classes into phylum
• Phylum into kingdom
• Rather than use all seven categories in naming
  organisms, Linnaeus chose to use the genus and
  specie names

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Linnaeus's System of Classification

• The two smallest categories, genus and species,
  were discussed in the example of the bears
• The giant panda, resembles the grizzly bear and
  the polar bear
• However, it differs enough from them and other
  species in the genus Ursus that it is placed in
  its own genus, Ailuropoda

15
Linnaeus's System of Classification

• The grizzly bear, Ursus arctos, and the polar
  bear, Ursus maritimus, are classified as
  different species in the same genus, Ursus
• The giant panda is placed in a separate genus

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Linnaeus's System of Classification
17
Linnaeus's System of Classification

• Genera that share many characteristics, such as
  Ursus and Ailuropoda, are grouped in a larger
  category, the familyin this case, Ursidae
• These bears, together with six other families of
  animals, such as dogs (Canidae) and cats
  (Felidae), are grouped together in the order
  Carnivora
• An order is a broad taxonomic category composed
  of similar families
• The next larger category, the class, is composed
  of similar orders
• For example, order Carnivora is placed in the
  class Mammalia, which includes animals that are
  warm-blooded, have body hair, and produce milk
  for their young

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Linnaeus's System of Classification

• Several different classes make up a phylum
  (plural phyla)
• A phylum includes many different organisms that
  nevertheless share important characteristics
• The class Mammalia is grouped with birds (class
  Aves), reptiles (class Reptilia), amphibians
  (class Amphibia), and all classes of fishes into
  the phylum Chordata
• All these organisms share important features of
  their body plan and internal functions
• Finally, all animals are placed in the kingdom
  Animalia
• The kingdom is the largest and most inclusive of
  Linnaeus's taxonomic categories
• Linnaeus named two kingdoms, Animalia and Plantae

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CLASSIFICATION
20
Linnaeus's System of Classification

• Linnaeuss hierarchical system of classification
  uses seven taxonomic categories
• This illustration shows how a grizzly bear, Ursus
  arctos, is grouped within each taxonomic category
• Only some representative species are illustrated
  for each category above the species

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Linnaeus's System of Classification
22
CLASSIFICATION
23
Modern Evolutionary Classification

• In a sense, organisms determine who belongs to
  their species by choosing with whom they will
  mate!
• Taxonomic groups above the level of species are
  invented by researchers who decide how to
  distinguish between one genus, family, or phylum,
  and another
• Linnaeus and other taxonomists have always tried
  to group organisms according to biologically
  important characteristics
• Like any taxonomic system, however, Linnaeus's
  system had limitations and problems

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Which Similarities Are Most Important?

• Linnaeus grouped species into larger taxa, such
  as genus and family, mainly according to visible
  similarities and differences
• But which similarities and differences are most
  important?
• If you lived in Linneaus's time, for example, how
  would you have classified dolphins?
• Would you have called them fishes because they
  live in water and have finlike limbs?
• Or would you call them mammals because they
  breathe air and feed their young with milk?
• How about the animals shown in the figure?
• Adult barnacles and limpets live attached to
  rocks and have similarly shaped shells with holes
  in the center
• Crabs, on the other hand, have body shapes unlike
  those of barnacles or limpets
• Based on these features, would you place limpets
  and barnacles together, and crabs in a different
  group?

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Which Similarities Are Most Important?

• Classifying species based on easily observed
  adult traits can pose problems
• Observe the crab (top left), barnacles (bottom
  left), and limpet (right)
• Which seems most alike?

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Which Similarities Are Most Important?
27
Evolutionary Classification

• Darwin's ideas about descent with modification
  have given rise to the study of phylogeny, or
  evolutionary relationships among organisms
• Biologists now group organisms into categories
  that represent lines of evolutionary descent, or
  phylogeny, not just physical similarities
• The strategy of grouping organisms together based
  on their evolutionary history is called
  evolutionary classification

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Evolutionary Classification

• Species within a genus are more closely related
  to each another than to species in another genus
• According to evolutionary classification, that is
  because all members of a genus share a recent
  common ancestor
• Similarly, all genera in a family share a common
  ancestor
• This ancestor is further in the past than the
  ancestor of any genus in the family but more
  recent than the ancestor of the entire order
• The higher the level of the taxon, the farther
  back in time is the common ancestor of all the
  organisms in the taxon

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Evolutionary Classification

• Organisms that appear very similar may not share
  a recent common ancestor
• Natural selection, operating on species in
  similar ecological environments, has often caused
  convergent evolution
• For example, superficial similarities once led
  barnacles and limpets to be grouped together, as
  shown on the left of the figure

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Evolutionary Classification Traditional
Classification and Cladogram

• Early systems of classification grouped organisms
  together based on visible similarities
• That approach might result in classifying limpets
  and barnacles together (left)

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Evolutionary Classification Traditional
Classification and Cladogram
32
Evolutionary Classification

• However, barnacles and limpets are different in
  important ways
• For example, their free-swimming larvae, or
  immature forms, are unlike one another
• Certain adult characteristics are different too
• Adult barnacles have jointed limbs and a body
  divided into segments
• Barnacles periodically shed, or molt, their
  external skeleton
• These characteristics make barnacles more similar
  to crabs than to limpets
• Limpets, in turn, have an internal anatomy that
  is closer to that of snails, which are mollusks
• And like mollusks, limpets do not shed their
  shells
• Because of such characteristics, taxonomists
  infer that barnacles are more closely related to
  crabs than to mollusks
• In other words, barnacles and crabs share an
  evolutionary ancestor that is more recent than
  the ancestor that barnacles share with limpets
• Thus, both barnacles and crabs are classified as
  crustaceans, and limpets are mollusks

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Classification Using Cladograms

• To refine the process of evolutionary
  classification, many biologists now prefer a
  method called cladistic analysis
• Cladistic analysis identifies and considers only
  those characteristics of organisms that are
  evolutionary innovationsnew characteristics that
  arise as lineages evolve over time
• Characteristics that appear in recent parts of a
  lineage but not in its older members are called
  derived characters

34
Classification Using Cladograms

• Derived characters can be used to construct a
  cladogram, a diagram that shows the evolutionary
  relationships among a group of organisms
• You can see an example of a cladogram on the
  right-hand side of the figure
• Notice how derived characters, such as
  free-swimming larva and segmentation, appear
  at certain locations along the branches of the
  cladogram
• These locations are the points at which these
  characteristics first arose
• You can see that crabs and barnacles share some
  derived characters that barnacles and limpets do
  not
• One such shared derived character is a segmented
  body
• Another is a molted external skeleton
• Thus, this cladogram groups crabs and barnacles
  together as crustaceans and separates them from
  limpets, which are classified as a type of mollusk

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Classification Using Cladograms Traditional
Classification and Cladogram

• Biologists now group organisms into categories
  that represent lines of evolutionary descent, or
  phylogeny, not just physical similarities
• Crabs and barnacles are now grouped together
  (right) because they share several
  characteristics that indicate that they are more
  closely related to each other than either is to
  limpets
• These characteristics include segmented bodies,
  jointed appendages, and an external skeleton that
  is shed during growth

36
Classification Using Cladograms Traditional
Classification and Cladogram
37
Classification Using Cladograms

• Cladograms are useful tools that help scientists
  understand how one lineage branched from another
  in the course of evolution
• Just as a family tree shows the relationships
  among different lineages within a family, a
  cladogram represents a type of evolutionary tree,
  showing evolutionary relationships among a group
  of organisms

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CLASSIFICATION

• Inferring Phylogeny
• Infer the probable evolutionary relationships
  among species that have been classified
• Sometimes a Phylogenetic Tree is used

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PHYLOGENETIC TREE
40
CLASSIFICATION

• Binomial name of a species is called its
  scientific name
• Describes the organism or the range of the
  organism, or honors another scientist or friend
• Classification
• Phylum used in animal classification
• Division used in plant classification
• Classification of species
• Subspecies (races) morphological different and
  are often geographically separated
• Varieties morphologically different and are
  often not geographically separated
• Some produced by humans (apples, peaches and
  nectarines)
• Strain biochemically dissimilar group within a
  species
• Usually used in reference to microorganisms

41
CLASSIFICATION

• Evidence Used in Classification
• Comparative morphology
• Embryology
• Homologous structures show evolutionary
  relationships between organisms (bones in the
  forelimb of a lizard are embryologically similar
  to those in a cat)
• Chromosomes
• Karyotypes compare numbers and shapes
• Biochemistry
• Sequence of bases in DNA
• Amino acid sequence in proteins
• Physiology
• Function of systems
• Phylogeny
• Evolutionary relationships
• Biosystematics
• Using reproductive compatibility to infer
  evolutionary relationships

42
Similarities in DNA and RNA

• All of the classification methods discussed so
  far are based primarily on physical similarities
  and differences
• But even organisms with very different anatomies
  have common traits
• For example, all organisms use DNA and RNA to
  pass on information and to control growth and
  development
• Hidden in the genetic code of all organisms are
  remarkably similar genes
• Because DNA and RNA are so similar across all
  forms of life, these molecules provide an
  excellent way of comparing organisms at their
  most basic leveltheir genes

43
Similarities in DNA and RNA

• The genes of many organisms show important
  similarities at the molecular level
• Similarities in DNA can be used to help determine
  classification and evolutionary relationships
• Now that scientists can sequence, or read, the
  information coded in DNA, they can compare the
  DNA of different organisms to trace the history
  of genes over millions of years

44
Similar Genes 

• Even the genes of diverse organisms such as
  humans and yeasts show many surprising
  similarities
• For example, humans have a gene that codes for
  myosin, a protein found in our muscles
• Researchers have found a gene in yeast that codes
  for a myosin protein
• As it turns out, myosin in yeast helps enable
  internal cell parts to move
• Myosin is just one example of similarities at the
  molecular levelan indicator that humans and
  yeasts share a common ancestry

45
DNA Evidence 

• DNA evidence can also help show the evolutionary
  relationships of species and how species have
  changed
• The more similar the DNA sequences of two
  species, the more recently they shared a common
  ancestor, and the more closely they are related
  in evolutionary terms
• And the more two species have diverged from one
  another, or changed in comparison to one another
  during evolution, the less similar their DNA will
  be

46
DNA Evidence

• Consider the case of the American vulture and the
  African vulture, which resemble each other
• Both birds have traditionally been classified
  together as vultures
• One group of birds inhabits Africa and Asia, and
  the other, the Americas
• But American vultures have a peculiar behavior
  When they get overheated, they urinate on their
  legs, and evaporative cooling removes some body
  heat
• The only other birds known to behave this way are
  storks, which look quite different from vultures
  and have always been put in a separate family
• Does this similarity in behavior indicate a close
  evolutionary relationship?

47
DNA Evidence

• Scientists analyzed the DNA of these three birds
• The analysis showed that the DNA sequences of the
  American vulture and the stork were more similar
  than those of the American vulture and the
  African vulture
• This similarity in DNA sequences indicates that
  the American vulture and the stork share a more
  recent common ancestor than do the American
  vulture and the African vulture
• Therefore, the American vulture is more closely
  related to storks than to other vultures

48
Molecular Clocks

• Comparisons of DNA can also be used to mark the
  passage of evolutionary time
• A model known as a molecular clock uses DNA
  comparisons to estimate the length of time that
  two species have been evolving independently
• To understand molecular clocks, think about a
  pendulum clock
• It marks time with a periodically swinging
  pendulum
• A molecular clock also relies on a repeating
  process to mark timemutation

49
Molecular Clocks

• Simple mutations occur all the time, causing
  slight changes in the structure of DNA, as shown
  in the figure
• Some mutations have a major positive or negative
  effect on an organism's phenotype
• These mutations are under powerful pressure from
  natural selection
• Other mutations have no effects on phenotype
• These neutral mutations accumulate in the DNA of
  different species at about the same rate
• A comparison of such DNA sequences in two species
  can reveal how dissimilar the genes are
• The degree of dissimilarity is, in turn, an
  indication of how long ago the two species shared
  a common ancestor

50
Molecular Clocks

• By comparing the DNA sequences of two or more
  species, biologists estimate how long the species
  have been separated
• What evidence indicates the species C is more
  closely related to species B than to species A?

51
Molecular Clocks
52
Molecular Clocks

• The use of molecular clocks is not simple,
  however, because there is not just one molecular
  clock in a genome
• Instead, there are many, each of which ticks at
  a different rate
• This is because some genes accumulate mutations
  faster than others
• These different clocks allow researchers to time
  different kinds of evolutionary events
• Think of a conventional clock
• If you want to time a brief event, you pay
  attention to the second hand
• To time an event that lasts longer, you use the
  minute hand or the hour hand
• In the same way, researchers would use a
  different molecular clock to compare modern bird
  species than they would to estimate the age of
  the common ancestor of yeasts and humans

53
Kingdoms and Domains

• As in all areas of science, systems of
  classification adapt to new discoveries
• Ideas and models change as new information arises
• Some explanations have been discarded altogether,
  whereas others, such as Darwin's theory of
  evolution by natural selection, have been upheld
  and refined through years of research
• So, it should not be surprising that early
  attempts at drawing life's universal tree were
  based on some misguided assumptions
• Some of the earliest trees of life were dominated
  by humans
• These models represented vertebrates as the most
  important and abundant animals
• They also implied that higher animals evolved
  from lower animals that were identical to
  modern forms
• Biologists now know these notions are incorrect

54
The Tree of Life Evolves

• The scientific view of life was simpler in
  Linnaeus's time
• The only known differences among living things
  were the fundamental traits that separated
  animals from plants
• Animals were mobile organisms that used food for
  energy
• Plants were green, photosynthetic organisms that
  used energy from the sun

55
Five Kingdoms 

• As biologists learned more about the natural
  world, they realized that Linnaeus's two
  kingdoms, Animalia and Plantae, did not
  adequately represent the full diversity of life
• First, microorganisms such as protists and
  bacteria were recognized as being significantly
  different from plants and animals
• Scientists soon agreed that microorganisms
  merited their own kingdom, which was named
  Protista
• Then, the mushrooms, yeasts, and molds were
  separated from the plants and placed in their own
  kingdom, Fungi
• Later still, scientists realized that bacteria
  lack the nuclei, mitochondria, and chloroplasts
  found in other forms of life
• Therefore, they were placed in another new
  kingdom, Monera
• This process produced five kingdomsMonera,
  Protista, Fungi, Plantae, and Animalia

56
CLASSIFICATION

• Five Kingdom System
• Monera
• Prokaryotic organisms
• Bacteria and blue-green algae
• Protista
• Eukaryotic organisms that lack specialized tissue
  systems
• Unicellular or multicellular
• Algae and protozoa
• Fungi
• Heterotrophic unicellular and multicellular
  eukaryotic organisms
• Plantae
• Eukaryotic, multicellular, autotrophic organisms
  with tissues
• Animalia
• Eukaryotic, multicellular, heterotrophic
  organisms with tissues

57
CLASSIFICATION
58
CLASSIFICATION
59
CLASSIFICATION
60
CLASSIFICATION
61
Six Kingdoms 

• In recent years, as evidence about microorganisms
  continued to accumulate, biologists came to
  recognize that the Monera were composed of two
  distinct groups
• Some biologists consider the differences between
  these two groups to be as great as those between
  animals and plants
• As a result, the Monera have been separated into
  two kingdoms, Eubacteria and Archaebacteria,
  bringing the total number of kingdoms to six

62
Six Kingdoms 

• The six-kingdom system of classification includes
  the kingdoms Eubacteria, Archaebacteria,
  Protista, Fungi, Plantae, and Animalia
• This system of classification is shown in the
  bottom row of the table

63
Six Kingdoms 

• This diagram shows some of the ways organisms
  have been classified into kingdoms over the years
• The six-kingdom system includes the following
  kingdoms Eubacteria, Archaebacteria, Protista,
  Fungi, Plantae, and Animalia

64
Six Kingdoms 
65
The Three-Domain System

• Some of the most recent evolutionary trees have
  been produced using comparative studies of a
  small subunit of ribosomal RNA that occurs in all
  living things
• Using a molecular clock model, scientists have
  grouped modern organisms according to how long
  they have been evolving independently

66
The Three-Domain System

• Molecular analyses have given rise to a new
  taxonomic category that is now recognized by many
  scientists
• The domain is a more inclusive category than any
  otherlarger than a kingdom
• The three domains are
• Eukarya which is composed of protists, fungi,
  plants, and animals
• Bacteria which corresponds to the kingdom
  Eubacteria
• Archaea which corresponds to the kingdom
  Archaebacteria
• As scientists continue to accumulate new
  information about organisms in the domains
  Bacteria and Archaea, these domains may be
  subdivided into additional kingdoms

67
The Three-Domain System

• Clearly, modern classification is a rapidly
  changing science, and we must pick a convention
  to classify life's diversity for the purposes of
  this Text
• In this Text, we recognize the three domains and
  also refer frequently to the six kingdoms
• The relationship between the three domains and
  the six kingdoms is shown in the table
• It also summarizes the key characteristics of
  each kingdom
• You can see that some groups share one or more
  traits with other groups

68
The Three-Domain System

• Organisms are grouped in three domains
• There is a simple relationship between the three
  domains and the six kingdoms
• This table summarizes key evidence used in
  classifying organisms into these major taxonomic
  groups

69
The Three-Domain System
70
Domain Bacteria

• The members of the domain Bacteria are
  unicellular and prokaryotic
• Their cells have thick, rigid cell walls that
  surround a cell membrane
• The cell walls contain a substance known as
  peptidoglycan
• The domain Bacteria corresponds to the kingdom
  Eubacteria
• These bacteria are ecologically diverse, ranging
  from free-living soil organisms to deadly
  parasites
• Some photosynthesize, while others do not
• Some need oxygen to survive, while others are
  killed by oxygen

71
Domain Archaea

• Also unicellular and prokaryotic, members of the
  domain Archaea live in some of the most extreme
  environments you can imaginevolcanic hot
  springs, brine pools, and black organic mud
  totally devoid of oxygen
• Indeed, many of these bacteria can survive only
  in the absence of oxygen
• Their cell walls lack peptidoglycan, and their
  cell membranes contain unusual lipids that are
  not found in any other organism
• The domain Archaea corresponds to the kingdom
  Archaebacteria.

72
Domain Eukarya

• The domain Eukarya consists of all organisms that
  have a nucleus
• It is organized into the four remaining kingdoms
  of the six-kingdom system
• Protista
• Fungi
• Plantae
• Animalia
• Organisms in these kingdoms are diverse and varied

73
Domain Eukarya

• The domains Bacteria and Archaea include the same
  organisms that are in the kingdoms Eubacteria and
  Archaebacteria
• The domain Eukarya includes the protists, fungi,
  plants, and animals
• Biologists continue to investigate how these
  three large groups originated
• Which domain includes organisms from more than
  one kingdom?

74
Domain Eukarya
75
Protista

• The kingdom Protista is composed of eukaryotic
  organisms that cannot be classified as animals,
  plants, or fungi
• Of the six kingdoms, Protista is the least
  satisfying classification, because its members
  display the greatest variety
• Most protists are unicellular organisms, but
  some, such as the multicellular algae, are not
• Some protists are photosynthetic, while others
  are heterotrophic
• Some share characteristics with plants, others
  with fungi, and still others with animals

76
Fungi 

• Members of the kingdom Fungi are heterotrophs
• Most feed on dead or decaying organic matter
• Unlike other heterotrophs, these fungi secrete
  digestive enzymes into their food source
• They then absorb the smaller food molecules into
  their bodies
• The most recognizable fungi, including mushrooms,
  are multicellular
• Some fungi, such as yeasts, are unicellular

77
Plantae 

• Members of the kingdom Plantae are multicellular
  organisms that are photosynthetic autotrophs
• In other words, they carry out photosynthesis
• Plants are nonmotilethey cannot move from place
  to place
• They also have cell walls that contain cellulose
• The plant kingdom includes cone-bearing and
  flowering plants as well as mosses and ferns
• Although older classification systems regard
  multicellular algae as plants, in this book we
  group algae with the protists

78
Animalia 

•  Members of the kingdom Animalia are
  multicellular and heterotrophic
• The cells of animals do not have cell walls
• Most animals can move about, at least for some
  part of their life cycle
• As you will see in later chapters, there is
  incredible diversity within the animal kingdom,
  and many species of animals exist in nearly every
  part of the planet