DIVERSITY OF EARTHS ORGANISMS AND CLADISTICS

1. DIVERSITY OF EARTH'S ORGANISMS(AND CLADISTICS)

2. 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.

3. 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.

4. 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.

5. 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.

6. 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).

7. 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.

8. 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.  

9. 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.

10. 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.

11. MONOPHYLETIC GROUP

12. 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.

13. POLYPHYLETIC GROUP

14. 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.

15. PARAPHYLETIC GROUP

16. 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.

17. 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.

18. HOMOLOGOUS STRUCTURES

19. 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). 

20. 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).

21. AN ADULT POLYPHEMUS MOTH WITH EYESPOTS

22. A COSTA RICAN BUTTERFLY OF THE GENUS CALIGO WITH EYESPOTS

23. 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.

24. EXAMPLE OF A CLADOGRAM

25. EXAMPLE OF A CLADOGRAM

26. 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.

27. 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. 

28. 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.

29. MATRIX OF TAXA VERSUS CHARACTERS

30. Cladogram that clusters the taxa that have shared derived characters.

31. 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.

32. 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). 

33. 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).

34. NEW MATRIX

35. NEW CLADOGRAM

36. 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

37. 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.

38. 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.

39. Brontosaurus vs. Apatosaurus