DIVERSITY OF EARTH'S ORGANISMS (AND CLADISTICS)

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DIVERSITY OF EARTH'S ORGANISMS(AND CLADISTICS)
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INTRODUCTION

• One of the goals of science is to recognize
  patterns and order in the natural world.  Are
  there patterns in the biota (sum total of all
  living organisms that have ever lived)?  Can we
  recognize any patterns that may be present and
  use the patterns to order the biota?  The answer
  to both of these questions is yes.  Can we use
  the patterns to help us understand Earth and
  biotic processes that account for the diversity
  of the biota?  Again, the answer is yes.
• The key to understanding the evolution and
  diversity of Earth's organisms is to determine
  their phylogeny (how they are related to each
  other and to the rest of the biota).  In order to
  do this we need to understand some of the
  principles of evolution, classification
  (taxonomy), and phylogeny.

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CONCEPTS AND TERMS

• PHYLOGENY  The history of descent of organisms
  (evolutionary relationships).
• TAXONOMY  The classification of organisms (the
  science of classifying organisms).  A grouping of
  organisms is called a taxon (taxa, plural). 
  Taxonomy is not just naming groups of organisms -
  species and higher taxa reflect evolution.
• ORGANIC EVOLUTION  The change of organisms over
  time.  As Darwin (1859) put it "Descent with
  modification".
• DIVERSITY  The different types of organisms. 
  Diversity of the biota (all organisms alive and
  extinct) is measured both in time and in space. 
  Diversity in time is reflected by evolutionary
  change.  Diversity in space is reflected by the
  geographic distribution of organisms
  (biogeography).
• BIOGEOGRAPHY  The geographic distribution of
  organisms.  For ancient organisms we use the term
  PALEOBIOGEOGRAPHY.

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SYSTEMATICS

• Refers to the combination of the above. 
  Systematics goes beyond just traditional taxonomy
  (naming and classification of organisms). 
  Systematists (scientists who study systematics)
  look at past and present geographic distributions
  of organisms (biogeography and paleobiogeography),
  diversity of both modern organisms and past
  organisms, evolutionary history, and the total
  pattern of natural diversity to provide the basic
  framework for all of biology and paleontology.

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HIERARCHY

•  We can organize the biota into a heirarchy (rank
  or order of the features of the biota).  For
  example Living Organisms -- things that are
  alive Vertebrates  -- living organisms that have
  a backbone Mammals living organisms that have
  a backbone and have fur and mammary glands.
• Thus mammals are a subset of all animals that
  have backbones.  All of the biota is connected by
  the sharing of features in a hierarchy.  Thus
  most organisms could be described as having a
  primitive body plan with variations  (but the
  original, unmodified body plan is always present
  in the biota).  Life is not really infinitely
  diverse, but is connect by the sharing of certain
  features in a hierarchy.

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CHARACTERS

• To recognize the heirarchy we must identify
  features of organisms.  These features are
  referred to as characters.  The distribution of
  characters among a selected group of organisms
  has meaning, but a single feature of a specific
  organism does not have much meaning (except to
  separate it from other organism).  Thus, shared
  characters among organisms are important in
  classifying them as belonging to groups of
  related organisms.
• General Characters (also called primitive
  characters) are characters of larger groups that
  are not specific to smaller groups within the
  larger group (for example, birds have a backbone
  this is not specific to birds because frogs
  also have a backbone and both birds and frogs
  inherited a backbone from a common ancestor that
  had a backbone).  Specific Characters (also
  called derived characters) are usually restricted
  to a smaller group within a larger group (thus
  feathers are specific to birds, which belongs to
  the larger group of vertebrates frogs, which are
  also vertebrates, do not have feathers and thus
  can not be grouped with birds using the specific
  character of possession of feathers).

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PHYLOGENY, HEIRARCHY, AND CLADISTICS

• Cladistics (also called Phylogenetic Systematics)
  is a form of systematics that attempts to
  determine the phylogenetic relationships of
  organisms based on unique shared characters.
• Cladists construct cladograms.  Cladograms are
  branching diagrams to show a hierarchical
  distribution of shared characters.  To construct
  cladograms we used shared observable characters
  (not functions we can't observe functions).
• We can group anything using shared characters,
  thus it is not restricted to living organisms. 
  However, when we group living organisms into a
  heirarchy based on shared characters, we are
  implying that the organisms have an evolutionary
  relationship (i.e. they share a common
  ancestor). 
• The history of descent of organisms is referred
  to as phylogeny. The phylogeny of a group of
  organisms shows the evolutionary relationships
  within the group.  Phylogenies are determined by
  constructing cladograms.

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CLADISTICS (CONT.)

• Each branch (or bundle of branches) of a
  phylogeny is called a clade (from clados meaning
  branch).  A divergence is a split on a
  cladogram.  Convergence is the evolution of
  similar features in two unrelated (or distantly
  related) clades.
• Groups of organisms shown on a phylogeny are
  called taxa (singular taxon).  For very detailed
  work, the species level taxon is used. 
  Biologists define species as a population of
  naturally interbreeding organisms (in other
  words, members of the same species share a common
  gene pool).  Of course, paleontologist cannot use
  this definition directly. Paleontologist define
  morphologic species. A morphologic species
  (morphospecies) is defined by similarity of
  anatomical or morphological characters within a
  fossil group.
•   So the manner in which organisms are related is
  defined as their phylogenetic relationships.  

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CLADISTICS (CONT.)

• In order to understand the history of life, we
  have to understand the patterns of evolution. 
  Darwinian evolution is the most accepted theory
  of evolution today.  First proposed by Charles
  Darwin (1859) in On the Origin of Species by
  Means of Natural Selection.
• This concept is sometimes expressed as "Survival
  of the Fittest", however, this expression is
  often misunderstood.  Survival of the fittest
  really means that the organisms that survive to
  reproduce, or reproduce more offspring than other
  members of their species, will selectively pass
  on more of their traits to their offspring (thus
  a change will occur in the gene frequencies of
  the gene pool, thus evolution will take place).
• For Darwinian evolution we use phylogenetic
  systematics (cladistics) to show evolutionary
  relationships of ancestors to descendants.

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CLADISTICS (CONT.)

• Evolution means descent with modification.  In
  order to understand the history of life, we have
  to understand the patterns of evolution.  We use
  phylogeny (Greek phylum tribe, genos birth
  or origin) to show relationships of ancestors to
  descendants, therefore, phylogeny explains the
  history of descent of organisms.
•      In modern phylogenetic methods, we use
  cladograms to show monophyletic groups (natural
  groups that descended from a common ancestor).
  Polyphyletic groups are groups that do not share
  a closest common ancestor, and thus are not of
  value in determining phylogeny.  Paraphyletic
  groups are groups that do not include all the
  descendants of a common ancestor.

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MONOPHYLETIC GROUP
From http//www.ucmp.berkeley.edu/glossary/gloss1
/phyly.html 
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CLADISTICS (CONT.)

• Evolution means descent with modification.  In
  order to understand the history of life, we have
  to understand the patterns of evolution.  We use
  phylogeny (Greek phylum tribe, genos birth
  or origin) to show relationships of ancestors to
  descendants, therefore, phylogeny explains the
  history of descent of organisms.
•      In modern phylogenetic methods, we use
  cladograms to show monophyletic groups (natural
  groups that descended from a common ancestor).
  Polyphyletic groups are groups that do not share
  a closest common ancestor, and thus are not of
  value in determining phylogeny.  Paraphyletic
  groups are groups that do not include all the
  descendants of a common ancestor.

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POLYPHYLETIC GROUP
From http//www.ucmp.berkeley.edu/glossary/gloss1
/phyly.html 
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CLADISTICS (CONT.)

• Evolution means descent with modification.  In
  order to understand the history of life, we have
  to understand the patterns of evolution.  We use
  phylogeny (Greek phylum tribe, genos birth
  or origin) to show relationships of ancestors to
  descendants, therefore, phylogeny explains the
  history of descent of organisms.
•      In modern phylogenetic methods, we use
  cladograms to show monophyletic groups (natural
  groups that descended from a common ancestor).
  Polyphyletic groups are groups that do not share
  a closest common ancestor, and thus are not of
  value in determining phylogeny.  Paraphyletic
  groups are groups that do not include all the
  descendants of a common ancestor.

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PARAPHYLETIC GROUP
From http//www.ucmp.berkeley.edu/glossary/gloss1
/phyly.html 
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EVOLUTION AS A FACT

•  If we, as scientists and students of science,
  are capable of understanding the world around us
  and the ways of science, then organisms have
  changed over time and have descended from a
  common ancestor. Therefore, Organic Evolution is
  a Fact.  Overwhelming evidence supports the
  Darwin-Wallace Theory of Evolution by Natural
  Selection.  Thus, natural selection is the
  primary means by which evolutionary change takes
  place.  Note  Creationist jump on the debate
  about evolution by scientists, but scientists
  argue the mechanisms and rates of evolution, not
  whether evolution has occurred.
• The biota has evolved!!!  As Darwin said, descent
  with modification.  The mechanism of evolution,
  as first proposed by Charles Darwin and Alfred
  Russell Wallace in a joint presentation to the
  Linnaean Society of London in 1858, is natural
  selection.
• Evolution (in morphology, genetic make-up,
  behavior, etc.) by natural selection involves
  modification such that ancestral (primitive)
  features (characters) are retained and new
  (derived) features are evolved.

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HOMOLOGUS STRUCTURES

•      Relationships in anatomical features is one
  line of evidence for the evolutionary
  relationship of organisms.  When two anatomical
  structures can be traced back to a single
  structure in a common ancestor, we say that the
  two structures are homologous. Thus homologous
  structures are called homologues (or
  homologies).  Thus, homology refers to two or
  more features that share a common ancestry.
• Our hands (as with all mammals) are homologous to
  the digits on dinosaur forelimbs and the common
  ancestor to both mammals and dinosaurs had digits
  on the forelimb.

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HOMOLOGOUS STRUCTURES
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ANALOGOUS STRUCTURES

• Analogues (Analogous Structures) perform a
  similar function in two different organisms, but
  may or may not trace back to a common ancestor. 
  For example, the wings of an insect and the wings
  of a bird are not homologues, but are analogues
  they also cannot be traced back to a single
  structure in a common ancestor (thus, they have a
  different embryological origin). 

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HOMOPLASTIC STRUCTURES

• Homoplastic structures look similar, but may or
  may not be analogous or homologous.
• Sometimes organisms evolve structures that look
  similar to structures in other organisms, but
  these structures cannot be traced back to a
  similar structure in the ancestors of two
  different organisms the structures may also not
  perform the same function in two different
  organisms, although they may look superficially
  similar. 
• One example of homoplasy is when organisms evolve
  structures that mimic the structures on other
  organisms (like large spots on the wings of a
  moth or butterfly that resemble eyes, perhaps to
  fool a potential predator).

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AN ADULT POLYPHEMUS MOTH WITH EYESPOTS
From http//www.npwrc.usgs.gov/resource/wildlife/
closlook/gntmoths.htm
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A COSTA RICAN BUTTERFLY OF THE GENUS CALIGO WITH
EYESPOTS
Photo by E. L. Crisp
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CLADOGRAMS AND THE RECONSTRUCTION OF PHYLOGENY

• Understanding evolution requires the recognition
  of homologous structures (including homologous
  molecular structures).
• Obvious (but often ignored) evidence of evolution
  is the hierarchical distribution of homologous
  characters in nature.  Some homologous characters
  are present in all organisms (such as DNA and/or
  RNA and cell membranes).  Some homologous
  characters are present in smaller groups.  And
  some homologous characters are restricted to very
  small groups.
• If evolution has occurred (and it has), there
  must be a single phylogeny.  We want to
  reconstruct evolutionary patterns.
• Cladograms are hierarchical branching diagrams
  that allow us to show shared derived characters
  (synapomorphies) that presumably relate
  organisms.  A cladogram is a testable
  hypothesis. 
• A cladogram specifies particular derived
  characters that are either present, or not
  present, in the organisms being compared.

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EXAMPLE OF A CLADOGRAM
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EXAMPLE OF A CLADOGRAM
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CLADOGRAMS (CONT.)

•      If derived characters are shared between two
  taxa, then cladistics argues that the two taxa
  are closely related.  Shared primitive characters
  do not reveal phylogenetic similarities.  Shared
  derived characters results in a cladogram that is
  monophyletic.  A monophyletic group includes the
  common ancestor and all the descendants of the
  common ancestor.  Polyphyletic groups do not
  share a most recent common ancestor.
•     How do we identify derived characters?  It is
  not always easy.  But..when a new taxon
  originates, it inherits features from its
  ancestor.  These inherited characters are
  primitive characters (plesiomorphs).  Features
  that arise for the first time in a new taxon are
  advanced characters or derived characters
  (apomorphies). These derived characters unite
  organisms (or fossils) into closely related
  groups, but only if the derived characters arose
  only once in related groups.  If the derived
  characters arose more than once (in unrelated
  groups) then the features are not representative
  of closely related groups.

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CLADOGRAMS (CONT.)

• In fact, evolutionary convergence is where
  derived characters have arisen more than once in
  different distantly related organisms.  For
  example, wings in birds, insects, and bats. 
  These groups are not closely related, but share
  derived characters (wings).  Of course, if we
  recognize that these are analogous structures,
  rather than homologous structures, we know the
  derived character of possessing wings does not
  necessarily relate these organisms.  So, we only
  want to compare homologous shared derived
  characters to show phylogenetic relationships. 
  Convergent evolution of characters presents the
  greatest threat to cladistic analysis.  We must
  recognize that convergence has occurred.
• Only homologous shared derived characters provide
  evidence of natural (monophyletic) groups.
•     A cladogram depicts monophyletic groups
  within monophyletic groups.  For example, warm
  bloodedness (endothermy) is ancestral
  (pleisomorphic) for Homo sapiens, but derived
  (apomorphic) for mammals.  We can add other
  organisms into the hierarchical scheme without
  altering the basic structure.
•     Therefore, a cladogram is a hypothesis of
  evolutionary relationships.

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CONSTRUCTING A CLADOGRAM

• The first thing that we want to do to show the
  evolutionary relationships of a group of
  organisms is to choose characters and construct a
  character matrix.
• For example, let us choose the following
  organisms for which we want to show the
  evolutionary relationships a clam (bivalve), a
  shark (cartilagenous fish), a bluegill (boney
  fish), a salamander (amphibian), an iguana
  (reptile-lizard), an alligator (reptile-archosaur)
  , a crow (bird), a racoon (mammal), and a human
  (mammal). 
• Now let us choose the characters that we are
  going to use to show the evolutionary
  relationships. 
• We will choose the following characters backbone
  (vertebral column or possession of vertebrae),
  bony skeleton, four limbs (2 pairs of appendages
  with digits at the end - the tetrapod condition),
  amniotic egg (egg with membrane and/or
  mineralized shell around an amniotic fluid that
  baths the embryo), hair, two openings in the
  skull behind the eye socket, and an opening in
  the skull in front of the eye socket (antorbital
  fenestra). 
• Now we will construct a table (matrix) of the
  taxa versus the characters.  If the organism has
  the character (derived condition) we will place a
  1 in the appropriate box, but if it doesn't
  (primitive condition) we will place a 0 in the
  box.

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MATRIX OF TAXA VERSUS CHARACTERS
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Cladogram that clusters the taxa that have shared
derived characters.
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CLADOGRAMS (CONT.)

•  Now we have a cladogram that is a hypothesis of
  the evolutionary relationships of the organisms
  that we have chosen. 
• Notice that the alligator and crow have a more
  recent common ancestor than the alligator and
  iguana, therefore, the alligator and the crow are
  more related in an evolutionary sense than is the
  alligator and iguana. 
• The clam does not share any of the derived
  characters (that we have chosen) with the other
  taxa and is considered the outgroup (for fixing
  polarizing the derived characters). 
• We could choose other characters to separate the
  human and racoon (like opposable thumb and large
  brain for humans and not for the racoon),
  however, this is not necessary just to group them
  together (as we see from the above cladogram). 
• We could also choose other characters to separate
  the alligator from the crow (like possession of
  feathers for the crow and not the alligator), but
  again, this is not necessary at this stage.

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PARSIMONY

•      If fewer steps in a cladogram provide an
  explanation of the derived characters, then we
  assume it is the correct cladogram until we have
  evidence to the contrary.   So, we start with the
  simplest hypothesis and consider it in the
  context of new or independent evidence (such as
  adding new characters or new taxa to our
  cladogram).
• HYPOTHESIS CLADOGRAM TEST NEW OR INDEPENDENT
  EVIDENCE (i.e. we consider more derived
  characters and more taxa and whether they fit the
  predictions made by the cladogram).
• Thus, cladograms are hypotheses.  They are more
  robust if they survive falsification attempts. 
  The addition of characters may result in the
  rejection of a certain cladogram (if the addition
  results in a character distribution which is not
  the most parsimonious). 

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CLADOGRAMS (CONT.)

• Now let us test the cladogram that we have
  presented above. 
• Let us predict that the Late Jurassic meat-eating
  (theropod) dinosaur Allosaurus is more closely
  related to the crow (thus birds) than to the
  alligator.
• We will look at the characters that we have
  already looked at, but we will need to add some
  more characters to test this hypothesis.  So, let
  us add Allosaurus to our table with the new
  characters added also.
• We we will add the following characters hole in
  the hip socket, 4th and 5th fingers on hand
  lost,  and three-toed foot (with digits 2, 3, and
  4).

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NEW MATRIX
Based on the additional characters that we have
added, our original hypothesis is supported by
the new data.  Thus, based on the data we have
looked at, we would conclude that Allosaurus has
a more recent common ancestor with the crow than
with the alligator. Our cladogram now may be
modified to include Allosaurus.
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NEW CLADOGRAM
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TAXONOMY

• Taxonomy is the process of classifying organisms
  into groups based on their similarities and of
  naming organisms.  Our present system of
  classification of organisms into major groups was
  devised by the Swedish naturalist Carolus
  Linnaeus (1707-1798).  The Linnaeus system of
  classification is a hierarchical scheme, as one
  proceeds up the classification ladder the
  categories become more inclusive. Cladistics may
  be used to get the evolutionary relationships
  then the organsims can be placed into the
  Linnaeus classification scheme. However, strict
  cladists prefer to name clades rather than to
  place the clades into the Linnaeus system.
• Major Subdivisions                        Example
  
• Kingdom                                       
  Animalia   Phylum                                
             Chordata      Subphylum               
                         Vertebrata        
  Class                                             
     Reptilia             Order                    
                             Theropoda
                   Family                          
                     Tyrannosauridae
                       Genus                       
                         Tyrannosaurus
                           Species                 
                            Tyrannosaurus rex

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BINOMIAL NOMENCLATURE AND CLASSIFICATION INTO
GROUPS

•      Linnaeus also said each organism should have
  two names (a binomen) to define it, the generic
  (genus) name and the specific (species) name. 
  For example, Tyrannosaurus rex or Homo sapiens
  (modern man).  Linnaeus, although not trying to
  show evolutionary relationships, lumped organisms
  that had similar traits into the same groups.  Of
  course, this implies phylogenetic relationships.
•      Modern biologists and paleontologists use
  cladistics to relate modern and fossil organisms
  in an evolutionary sense (i.e., determine their
  phylogenies).  They still name organisms based on
  the Linnaean system and may place their
  phylogenetic groupings into the Linnaean
  hierarchy.  However, biologists and
  paleontologists recognize the arbitrary nature of
  the Linnaean categories (for example, some
  paleontologists might refer to Saurischia as an
  order of the Dinosauria, whereas others may
  consider it to be a superorder), and thus may
  prefer that groupings on cladograms not be placed
  in formalized Linnaean categories.  On the other
  hand, some biologists and paleontologist do
  prefer to use the Linnaean system, once the
  evolutionary relationships have been worked out
  using cladistics.

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BINOMIAL NOMENCLATURE AND CLASSIFICATION INTO
GROUPS (CONT.)

•     However, biologists and paleontologists
  always name organisms at the genus and species
  level according to the Linnaean system and must
  follow international codes of zoological and
  botanical nomenclature (for example, the
  International Code of Zoological Nomenclature.
  The International Code of Zoological Nomenclature
  provides the rules that must be used when naming
  animals (a similar code exists for naming
  plants).  Names at the genus and species level
  are latinized and italicized (or underlined). 
  Particular endings are required for different
  Linnaean categories (for example order usually
  has the suffix a family has the suffix idae,
  etc.).  However, there is much freedom in the
  naming of organisms. For example a big
  carnivorous dinosaur found by John Osborn in 1905
  in Montana that was different than all other
  carnivorous dinosaurs known then was named
  Tyrannosaurus rex, meaning Tyrant Lizard King
  or King of the Tyrant Lizards (Note This is the
  type specimen for T. rex, to which all others
  must be compared, and is now housed at the
  Carnegie Museum of Natural History in
  Pittsburgh).
•      Priority of the name is another rule of
  naming organisms.  No two different organisms
  (extant or extinct) can have the same scientific
  name (binomen).  Also if two organism belong to
  the same taxon, they cannot be given different
  names the one that was named first is the
  correct name.  For example, the Yale
  paleontologist O.C. Marsh in 1877 named a partial
  sauropod dinosaur skeleton (found in Colorado) to
  the genus Apatosaurus (deceptive lizard).  A
  couple of years later (1879) he found an almost
  complete skeleton of a sauropod dinosaur in
  Wyoming and gave it the genus name Brontosaurus
  (thunder lizard).  Many years later, it was
  determined by paleontologists that the two
  skeletons were of the same creature, thus
  Apatosaurus was ruled to be the correct genus
  name by priority.

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Brontosaurus vs. Apatosaurus