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 life is to determine the phylogeny of the biota (how organisms, past and present, are related to each other).  In order to do this we need to understand the principles of evolution, classification (taxonomy), biogeography, and phylogeny.

PHYLOGENY:  The history of descent of organisms.

TAXONOMY:  The classification of organisms.

EVOLUTION:  The origin and change of organisms over time.

BIOGEOGRAPHY: The geographic distribution of organisms.  For ancient organisms we use the term PALEOBIOGEOGRAPHY.
 

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.

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 form other organism).  Thus, shared characters among organisms are important in classifying them as belonging to group of related organisms.

     General 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).  Specific Characters are usually restricted to a smaller group within a larger group (thus feathers are specific to bird, 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).
 

Phylogeny, Hierarchy,  and Cladistics ( Journey into the World of Cladistics)

     Cladistics (also called Phylogenetic Systematics) is a form of systematics that attemps 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 (see the example for vehicles in Fastovsky and Weishampel).  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 their evolutionary relationships.  Phylogenies are determined by constructing cladograms.

     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.  (Note:  Biologists define species as a population of naturally interbreeding organisms.  Of course, paleontologist cannot recognize interbreeding populations of ancient organisms directly.  Paleontologist often recognize morphologic species in practice, however, they should define species as a natural taxon the same way biologists do.  A morphologic species is defined by similarity of morphological characters within a fossil group.

     So the manner in which organisms are related is defined as their phylogenetic relationships.
 

Organic Evolution

     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.  For Darwinian evolution we use phylogeny to show relationships of ancestors to descendants.

     Evolution means descent with modification.  In order to understand the history of life, we have to understand the patterns of evolution (we will be more concerned with the patterns of evolution than the mechanism 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.

     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. Therefore, Organic Evolution is a Fact (Fastovsky and Weishampel, 1996).  [Note:  Creationist jump on the debate about evolution (for example: the debate about phyletic gradualism versus punturated equilibrium) by scientists, but scientists argue the mechanism 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.

     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.

     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.

    Analogues (Analogous Structures) cannot be traced back to a single structure in a common ancestor.  For example, the wings of an insect and the wings of a bird are not homologues, but are analogues; they cannot be traced back to a single structure on a common ancestor (thus, they have a different embryological origin).

     Understanding evolution requires the recognition of homologous anatomical 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 cell membranes).  Some homologous characters are present in smaller groups.  And some homologous characters are very restricted to small groups.
 

Cladograms and the Reconstruction of Phylogeny

     If evolution has occurred (and it has), there must be a single phylogeny.  In this course we will normally not use “Trees of Life” or “Evolutionary Trees”, but we will primarily use cladistics (also called Phylogenetic Systematics) (Journey into the World of Cladistics) to show relationships among organisms and thus reconstruct phylogeny based on these relationships.  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.  We can't test an “evolutionary tree”.  How can we ever know for sure that a particular organism is ancestral to another (see Paleobiology 22(2) - Foote  ).  A cladogram specifies particular derived characters that are either present, or not present, in the organisms being compared.

     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 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.

     In fact, evolutionary convergence is where derived characters have arisen more than once.  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.
 

Parsimony

     If fewer steps in a cladogram provide an explanation of the derived characters, then we assume it is the correct cladogram.

    So, we start with the simplest hypothesis and consider it in the context of new or independent evidence.

HYPOTHESIS: CLADOGRAM
TEST: NEW OR INDEPENDENT EVIDENCE (i.e. we consider more derived characters and whether they fit the cladogram).

Bird, Human, Bat example.

     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).

     Can we really test a “tree of life” (“evolutionary tree”).  Isn't it more of a story, rather than a testable scientific hypothesis.
 
 

Other Methods of Determining Phylogenetic Relationships

Phenetic Phylogeny

     Until recently (the last couple of decades) most biologists and paleontologists used a method of phylogenetic analysis known as phenetic phylogeny.  In phenetic phylogeny comparisons are made between  taxons based on overall similarity.  Both primitive (plesiomorphic) and derived (apomorphic) characters are used in this method.  Whether characters are homologues or analogues is basically ignored.  Computers are used to compare a large number of randomly chosen characters (usually 50 or more).  The characters are clustered using coefficients of similarity among different taxons.  From this the phylogeny is constructed.  This method is objective and repeatable, but may not always show the best evolutionary relationships.

Stratophenetic Phylogeny

     Based on the phenetic phylogeny (as discussed above), a stratophenetic phylogeny assumes that the evolutionary changes between ancestor and descendent is not so great as to seem implausible during the time interval between ancestor and descendent.  This method assumes a particular ancestor gave rise to a specific descendent.  Thus, “evolutionary trees” (or “trees of life”) were constructed using this method.  Until recently this was the most common method of phylogenetic analysis by paleontologists (and is still used by some paleontologists).

     In using a stratophenetic phylogeny approach, it is assumed that the ancestor will be represented by fossils older than fossils of the descendent.  The main problem with stratophenetic phylogeny is that the fossil record is incomplete, so we cannot be sure that older fossils with similar features were the direct ancestors to descendants (In theory, we should find a gradation of one type of organism to its related descendants, but in practice there are many “missing links” in the fossil record).   Because of this problem, many paleontologists no longer use stratophenetic phylogeny methods.

    Many modern paleontologists use the method of cladistic phylogeny.  In cladistic phylogeny the time ranges of taxa are not incorporated into the cladogram.  The phylogeny is based only on shared derived characters (synapomorphies) among the fossil taxa being compared.
 

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.

Major Subdivisions                        Example

Kingdom                                        Animalia
  Phylum                                           Chordata
     Subphylum                                      Vertebrata
        Class                                                Reptilia
            Order                                               Theropoda
                 Family                                             Tyrannosauridae
                     Genus                                              Tyrannosaurus
                         Species                                            Tyrannosaurus rex
 

Binomial Nomenclature

     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 paleontologists use cladistics, evolutionary systematics, or phenetics to relate 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, some paleontologists recognize the arbitrary nature of the Linnaean terms (for example, some might refer to Saurischia as an order of the Dinosauria, whereas others may consider it to be a superorder), and thus  prefer to not refer groupings on cladograms into formalized Linnaean categories above the family level (many do though).

    However, all paleontologists do name fossils at the genus and species level according to the Linnaean system and must follow the International Code of Zoological Nomenclature for animals and the International Code of Botanical Nomenclature for plants.  The International Code of Zoological Nomenclature and the International Code of Botanical Nomenclature provides the rules that must be used when naming animals and 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 [holotype] 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 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.
 

Microevolution versus Macroevolution

   Paleontologists think of two levels of evolution:

         Microevolution – the origin of new species, and
        Macroevolution – evolution above the level of species (origin of new genera,
                                      families, orders, etc.

    A large number of fossils are needed to recognize evolution at the microevolution level.  We try to document the change of organisms in short periods of time (100,000 to 1,000,000 years).  Macroevolution does not require such a large or complete fossil record.  However, we must always keep in mind that evolutionary change is always initiated at the species level.

     Evolution of the class Aves (birds) from dinosaurs is a good example.  Clear evidence of the similarities between birds and dinosaurs is evident from the fossil record, even though the fossil record is very incomplete for the transition from dinosaur to bird.  The 150 million year old Archaeopteryx from the Upper Jurassic rocks of Germany looks like a small crow sized dinosaur, but had clear impressions of feathers preserved (It is presently referred to as the first bird).  Recently, dinosaurs found in China show feather impressions (Are they birds or dinosaurs?).