Supplemental Lecture (97/10/15 update) by Stephen T. Abedon (

  1. Chapter title: Classification of Organisms
    1. A list of vocabulary words is found toward the end of this document
    2. Organismal diversity is the product of evolution. Evolutionary paths are branched and numerous, though most arrive at dead ends with organisms which do not survive in the face of environmental change. In this lecture we consider these evolutionary paths (called lineages), ignoring for the moment the processes that carry organisms along them.
    3. While the lineage of any given organism may have twisted repeatedly according to the whims of chance and change, key nodes may nevertheless be tracked retrospectively. These nodes consist of times of identifiable change, particularly points of divergence between two lineages (speciation events). The delineation of these nodes in organismal lineages is accomplished through fossil reconstruction of the past as well as by comparing extant organisms, looking for similarities and differences in anatomies, physiologies, genes, behaviors, etc. From this information classification and phylogenetic reconstruction is accomplished.
    4. In this lecture we will broadly review how organisms are systematically classified, plus how it is that classified organisms might be compared.
  2. Overview, Classification of Organisms
    1. The following is quoted from Prescott et al., 1996 (p. 390):
      1. In order to make sense of the diversity of organisms, it is necessary to group similar organisms together and organize these groups in a non-overlapping hierarchical arrangement. Taxonomy is the science of biological classification.
      2. The basic taxonomic group is the species, which is defined in terms of either sexual reproduction or general similarity.
      3. Morphological, physiological, metabolic, ecological, genetic, and molecular characteristics are all useful in taxonomy because they reflect the organization and activity of the genome. Nucleic acid structure is probably the best indicator of relatedness because nucleic acids are either the genetic material itself or the products of gene transcription.
      4. Classifications are based on any analysis of possible evolutionary relationships (phylogenetic or phyletic classification) or on overall similarity (phenetic classification).
  3. Linnaeus, Carolus (late 1700s)
    1. Classification according to similarity:
      1. Carolus Linnaeus developed a system of classification of every (then) known organism.
      2. This system is based on creating and differentiating groups in terms of structural (and other) similarities and differences.
    2. Linnaeus also invented binomial nomenclature to keep track of group members.
  4. Systematics
    1. Systematics is the study of the diversity of organisms and their evolutionary relationships.
    2. Science of classification:
      1. Systematics is the science of the classification of organisms.
      2. The main goal of systematics is the discovery and codification of phylogenetic relationships between organisms.
      3. "The term systematics often is used for taxonomy. However, many taxonomists define it in more general terms as 'the scientific study of organisms with the ultimate object of characterizing and arranging them in an orderly manner.' Any study of the nature of organisms, when the knowledge gained is used in taxonomy, is a part of systematics. Thus (systematics) encompasses disciplines such as morphology, ecology, epidemiology, biochemistry, molecular biology, and physiology." (p. 391, Prescott et al., 1996)
  5. Taxon [sing., taxa, pl.]
    1. A taxon is a phylogenetic grouping of organisms.
  6. Taxonomy
    1. Identification and classification:
      1. Taxonomy is the science concerned with the:
        1. identification
        2. classification
        3. nomenclature
      2. of organisms.
      3. "Taxonomy [Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern] is defined as the science of biological classification. In a broader sense it consists of three separate but interrelated parts: classification, nomenclature, and identification." (p. 391, Prescott et al., 1996)
    2. Note that the terms systematics and taxonomy can often be used semantically in a nearly indistinguishable manner.
  7. Identification
    1. Identification is "the practical side of taxonomy, the process of determining that a particular (organism) belongs to a recognized taxon." (p. 391, Prescott et al., 1996)
  8. Classification
    1. Classification is "the arrangement of organisms into groups or taxa." (p. 391, Prescott et al., 1996)
  9. Nomenclature
    1. Name assignment:
      1. Nomenclature is "the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules." (p. 391, Prescott et al., 1996)
      2. Note that ideally names have taxonimic meaning, i.e., they give clues to phylogenetic relationships.
  10. Hierarchical classification
    1. Hierarchy of designations:
      1. The full description of a given organism's place among all the world's organisms does not end with its binomial designation.
      2. There exists a hierarchy of designations only the last of which describe genera and species denomination.
      3. "A category in any rank unites groups in the level below it based on shared properties." (p. 391, Prescott et al., 1996)
    2. The major designations, listed in terms of increasing specificity, include:
      1. domain (empire/super-kingdom)
      2. kingdom
      3. phylum
      4. class
      5. order
      6. family
      7. genus
      8. species
    3. Various mnemonics exist to help you remember these designations from kingdom through species (many of which I apologize for and none of which I authored) including:
      1. Darn Kids Picking Cacti On Fridays Get Stuck
      2. Did King Phillip Comes Over For Great Sex?
      3. Do Kiss Pigs Carefully Or Face Grimy Smiles
      4. Do Kings Play Chess On Fine Grained Sand
      5. Did King Phillip Came Over From Germany Stoned? \
      6. Did King Peter Came Over From Geneva Switzerland?
      7. Do Kindly Produce Credit Or Furnish Good Security
      8. Do Keep Peeling Cold Onions For Good Smells
      9. Do Keep Putting Coal On the Fire Grate Slowly
      10. Did King Phillip Cry, "Oh, For Goodness Sake!"?
      11. Do Keep Putting Cheese On Five Green Spoons
      12. Did Karen's Pups Chew On Furry Grey Squirrels?
      13. Did King Phillip Come Over For Good Spaghetti?
      14. Did King Phillip Court Ophelia For Good Sex?
      15. Did Karl Push Cliff Over Football Grand Stand?
      16. Did King Peter Come Over From Germany Saturday?
      17. Do Kings Play Chess On Fat Girl's Stomach
      18. Do Keep Privates Clean Or Forget Getting Sex
    4. Objective/subjective classification:
      1. "Of all the categories in this classification system, only the lowest level, the species, is objective; that is, biologists can test whether two different populations of individuals represent two different species by testing whether they can interbreed successfully in nature. (As we have seen), however, (often) even that definition is difficult to apply." (p. 434, Postlethwait & Hopson, 1995)
      2. In practice the designation of species to taxons may appear somewhat arbitrary. In other words, such designations are subjective.
    5. Subjective taxon breadth:
      1. Different taxonomic categories (except that of domain) often have completely different meanings across different lineages (sizes, breadths, etc.).
      2. I suppose an ideal situation would be if taxonomic categories reflected some objective component such a time, but they don't (and that, unfortunately, is that).
    6. Note that it is very common, especially in informal situations, for informal names to be substituted for formal ones.
    7. We may speak of "apes" where more formally we would employ the superfamily designation Hominoidea.
    8. We may speak of "pseudomonads" where more formally we would employ the genus designation Pseudomonas.
  11. Classification of humans
    1. By way of example, we (humans) are classified as:




    criteria for














    notochord containing





    spinal chord containing





    hair and breasts





    nails, grasping digits, binocular vision





    apes and humans





    genus Homo, genus Australopithecus





    our genus





    our species



  12. Phylogeny [phylogenetic group]
    1. A phylogeny is a representation of organisms based on and describing evolutionary relationships.
  13. Monophyletic
    1. A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor which is a member of the same phylogenitic group, and which consists of all of the (known or considered) descendants of that common ancestor.
    2. A monophyletic taxon is a good taxon in an evolutionary sense, meaning that no members which ought to be a part of the taxon, in terms of ancestor-descendant relationships, are excluded.
    3. Symbolic examples:
      1. For example, if both B and C are descendants of A, then a monophyletic taxon would consist of all three species.
      2. For example, if both C and D are descendants of B, and B is a direct descendant of A, then a monophyletic taxon of these species could consist either of all four species, or of just species B, C, and D.
  14. Polyphyletic
    1. A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor, but in which one or more common ancestor is not a member of the same phylogenitic group, and that missing common ancestor is the most recent common ancestor.
    2. Evolutionarily bad as you can get taxon:
      1. A polyphyletic taxon is essentially an erroneously compiled taxonic grouping.
      2. It means that two unrelated taxa have been lumped into one. This can only be done if one includes the common ancestor, but then the resulting taxon would be either monophyletic or paraphyletic.
    3. Symbolic examples:
      1. For example, if both B and C are descendants of A, then a polyphyletic taxon would consist of just species B and C, i.e., species A would be left out.
      2. For example, if both C and D are descendants of B, and B is a direct descendant of A, then a polyphyletic taxon would be one consisting of just species C and D.
  15. Paraphyletic
    1. Missing member:
      1. A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor, but which does not include all of the known or considered descendants of that common ancestor.
      2. In the usage of cladists, a paraphyletic taxon is a monophyletic taxon in which a member, other than the most recent common ancestor, is excluded.
    2. Typically paraphyletic taxa represent the improper exclusion of members on the basis of phenotypic differences rather than on the basis of ancestor-descendant relationships.
    3. Symbolic examples:
      1. For example, if both B and C are descendants of A, then a paraphyletic taxon would consist of just species A and C or A and B, but not A, B, and C or just B and C.
      2. For example, if both C and D are descendants of B, and B is a direct descendant of A, then a parephyletic taxon would be one consisting of just species A, B, and C or just species A, B, and D, or just species B and C or B and D. In other words, any combination except one which includes both species C and D.
    4. Real examples:
      1. Birds and reptiles represent a paraphyletic taxon relative to mammals, though considering only birds, reptiles, and mammals, the three together form a monophyletic taxon (i.e., the reptiles are the ancestors of all reptiles, all mammals, and all birds).
      2. Reptilia alone is paraphyletic since it excludes mammals and birds as well as dinosoars, etc.
      3. Closer to home, Pongidea is paraphyltic because it includes the apes but excludes humans. Paraphyletic taxa represent flawed phylogenetic interpretations.
  16. Clades
    1. "The purpose of phylogenetic studies is to establish the evolutionary relationships among different species. In particular, we are interested in the identification of natural clades. A clade is defined as a group of species that share a common ancestor, which is not shared by another species outside of the clade." (pp. 118-119, Li and Graur, 1991)
    2. Monophylectic taxon:
      1. In other words, a clade is a monophyletic taxon.
      2. Clades are the only phylogenetically/evolutionarily real taxons.
      3. Other, non-monophyletic (e.g., paraphyletic) taxons are based on, for example, just morphological similarities rather than evolutionary relationships.
    3. Example: reptiles do not form a natural clade:
      1. The reptiles do not represent a true clade because, while there may be strong evolutionary relationships within this group, there are also a number of taxa which evolved from within this taxa but which are not included in the taxa reptiles
      2. Examples of these latter taxa include the birds, the mammals, and the dinosaurs as well as a number of extinct lineages.
    4. Example: apes + humans form a clade:
      1. The designation apes, like reptiles, does not form a true clade, though here this problem is easily corrected simply by accepting that humans are modified apes (just as apes are modified mammals and mammals are modified reptiles and reptiles are modified amphibians and amphibians are modified fish, etc.).
      2. That is, humans plus those animals typically classified as apes together form a monophyletic taxon, i.e., a clade.
  17. Non-arbitrary classification
    1. Ideally, the classification of organisms is done in a non-arbitrary manner.
    2. "Taxonomists generally choose characteristics in such a way that the groupings reflect some hierarchical principle of nature. But there's a catch: taxonomists disagree about which principle to emphasize." (p. 434, Postlethwait & Hopson, 1995).
    3. The two competing approaches are referred to as phenotypic and phylogenetic classification.
  18. Phenotypic [phenetic] classification
    1. Classified by looks:
      1. Phenotypic classification is concerned with grouping individual species into phenotypic categories (taxons) based on how organisms "look," "look" broadly defined.
      2. Note that once upon a time in the not so distant past taxonomists were not equipped to classify beyond the level of phenotypic groupings except via inference from phenotypic similarities.
    2. Evolutionary dissonance:
      1. Phenotypic similarity and evolutionary relationship do not always map one to one upon each other.
      2. In particular, phenotypic comparison can be an imperfect indicator of evolutionary relationship due to:
      3. complex correspondences between phenotype to genotype
      4. the occurrence of convergent evolution
      5. variations between lineages in rates and modes of phenotypic evolutionary change
  19. Phylogenetic [phyletic] classification
    1. Phylogenetic classification is concerned with grouping individual species into evolutionary categories.
    2. Since the early 1980's (or so) phylogenetic classfication has been made much more facile by the invention of molecular taxonomy: The evolutionary classification of organisms based on the nucleotide sequence divergence at individual loci (genes).
    3. Close, though not perfect:
      1. While classification employing nucleic acid sequence information can be non-arbitrary (i.e., classification is dependent only upon what classifying algorithm is employed), the phylogenies produced nevertheless tend to be approximations of evolutionary relationships rather than final words on the matter.
      2. This is one reason disagreement can exist even among molecular taxonomists.
      3. However, as more and more sequence is utilized in producing a phylogeny the associated uncertainty tends to decline.
    4. Phylogeny from phenotype:
      1. Note that very often these two approaches (phenotypic and phylogenetic classification) fully agree. This is because there usually is a correlation between evolutionary relatedness and phenotypic relatedness.
      2. However, such things as convergent evolution can really throw a wrench between the two classification philosophies since convergent evolution, by definition, produces phenotypic similarity in the absence of close evolutionary relatedness.
      3. The trick to solving these discrepancies is to concentrate on true homologies and ignore convergence.
      4. This is easier to say than to implement, however.
    5. Conflicts between phenotypic and phylogenetic classification are at the root of the various monophyly-paraphyly debates.
  20. Cladistics
    1. Cladistics is a method of phylogenetic classification which attempts to limit comparisons within groups only to those characters which are thought to have evolved within a given group, also known as derived characters.
    2. Unique homologous traits:
      1. Cladists consider only homologous traits, that is, those shared because of a common ancestry.
      2. However, the homologous traits which supply the most information to a cladist are those which are unique to the group under consideration (i.e., are not found or not found in the same form in groups ancestral to the group under consideration).
    3. A Cladist would consider the presence of wings to lump together two species as birds but not the presence of wings to lump bats with birds (different embryonic and therefore evolutionary origin).
    4. The cladist would not use the presence of eyes in all birds as evidence of unique evolutionary relatedness since eyes are thought to have evolved once in the vertebrate lineage and therefore to be common to the ancestors of both birds and bats (though the evidence for a similar embryonic origin and structure of bird and bat eyes could be considered evidence for the relatedness of bats and birds, as well as both to other types of vertebrates).
  21. Cladogram
    1. Graphical representation:
      1. Phylogenies are often presented as cladograms with their familiar branches and nodes.
      2. In other words, a cladogram is a graphical representation of a phylogeny.
    2. The universal tree is an example of a cladogram.
  22. Phylum [sing., phyla, pl.]
    1. A phylum is higher level animal taxon.
    2. "A group of animals or in some classifications plants sharing one or more fundamental characteristics that set them apart from all other animals and plants and forming a primary category of the animal or plant kingdon ."
  23. Division
    1. A division is the equivalent to phylum in plants.
  24. Ancestral characteristic
    1. An ancestral characteristic is a modified character shared between two groups and present in their common ancestor(s) in an unmodified form.
    2. An example in which the ancestral characteristic is considered is with bird feathers and mammalian hair, both of which are modifications on the reptilian scale. In this case the reptilian scale is considered to be the ancestral characteristic.
  25. Derived characteristics
    1. A derived characteristic is a novel modification of the ancestral form. Thus, in the above example, both hair and feathers represent derived characteristics.
    2. The sharing of presumptive derived characteristics is considered by cladists to be important evidence of evolutionary relatedness.
  26. Vocabulary
    1. Ancestral characteristic
    2. Animalia
    3. Chordata
    4. Clades
    5. Cladistics
    6. Cladogram
    7. Classification
    8. Classification of humans
    9. Derived characteristic
    10. Division
    11. Hierarchical classification
    12. Hominidae
    13. Hominoidea
    14. Homo
    15. Identification
    16. Linnaeus
    17. Mammalia
    18. Monophyletic
    19. Nomenclature
    20. Paraphyletic
    21. Phenetic classification
    22. Phyletic classification
    23. Phylogenetic classification
    24. Phylum
    25. Polyphyletic
    26. Primates
    27. sapiens
    28. Systematics
    29. Taxa
    30. Taxon
    31. Taxonomy
    32. Vertebrata
  27. Practice questions
  28. Note: Almost without exception the following questions are applicable to biology 113 and not microbiology 509.
    1. What's the difference between phenotypic and phylogenetic classification? [PEEK]
    2. Fill in the blanks: [PEEK]
    3. Eukarya     ---   Domain     
      Animalia    ---   Kingdom    
      __________  ---   Phylum     
      Vertebrata  ---   Subphylum  
      __________  ---   Class      
      Primates    ---   __________ 
      Hominoidea  ---   Superfamily
      Hominidae   ---   Family     
      Homo        ---   Genus      
      Sapiens     ---   Species    
    4. Draw a cladogram and circle what you would consider to be a hypothetical paraphyletic taxonomic grouping. Be sure I can distinguish extant from extinct species. [PEEK]
    5. In terms of human classification, fill in the blanks: [PEEK]
    6. Eukarya     ---   nucleated cells             
      Animalia    ---   animals                     
      __________  ---   notochord containing        
      Vertebrata  ---   spinal chord containing     
      Mammalia    ---   __________ & __________     
      Primates    ---   nails, grasping digits, etc.
      __________  ---   apes and humans             
      Hominidae   ---   bipedal apes   
    7. Except for species, taxonomic categories are subjectively defined. This is a consequence of systematics in general and taxonomy in particular being a typically human enterprise, complete with inconsistent solutions to ambiguous or conflicting data. However, at least in theory taxonomic categories are based upon unambiguously shared evolutionary relationships. What exactly does a shared evolutionary relationship mean?[PEEK]
    8. Fill in the blanks assuming proper hierarchical order: domain, kingdom, __________, class, ___________, family, __________, species. [PEEK]
    9. Phylogenies are supposed to reflect evolutionary relationships, but __________ classification methods can result in paraphyletic taxa. [PEEK]
    10. Given a phylogeny in which G is a common ancestor to A, B, C, D, E, and F (all distinct species); E is a common ancestor to A and B (but not C, D, E, F, or G); F is a common ancestor to C and D (but not A, B, E, F, or G); A is not an ancestor to B, C, or D; B is not an ancestor to A, C, or D; C is not an ancestor to A, B, or D; and D is not an ancestor to A, B, or C, draw a representative cladogram and circle a paraphyletic taxon. [PEEK]
    11. A hypothetical group of Seussian organisms has genetically determined digits on the end of their tails that number from 2 to 10 and which provide a defensive mechanism (that is, they poke carnivores in the eyes). The number of digits is not under selective pressure except that the number must be greater than one (since carnivores have more than one eye). It has been demonstrated by Dr. Harvy Fumblegun that individual mutations which change digit number (to anything but zero) can change digit number only in single steps of one digit each. Thus, a four digit organism can evolve directly into a three or five digit organism, but not directly into a six or two digit organism (that is, except via multiple mutational steps). By the phylogenetic species concept, Dr. Fumblegun has declared that digit number distinguishes species. In fact, digits apparently are involved in mating such that digit number serves as an isolating mechanism: individuals are able to mate solely with individuals possessing the same number of digits (something about poking each other in each other's collective eyes during copulation given the absence of corresponding digits used to block with). Given six extant species, A, B, C, D, E, and F, possessing respectively 2, 3, 4, 5, 8, and 10 tail digits each, draw a cladogram representing a phylogeny showing the evolutionary relationship of all of these organisms which additionally contains two (i.e., greater than one, less then three) monophyletic taxa which are not nested (i.e., one does not fit within the other) and which possess more than one extant species each (i.e., two or more per monophyly). Circle these monophyletic taxa, and be sure to label your extant species with the appropriate letter names. Be sure also to include the common ancestor to all of these species, explicitly show all species whether extinct or extant, and indicate the digit number of any extinct species you represent. (hint for drawing phylogeny: start with the extant species lined up in a row and then work backward in time connecting extant species with ancestral species through one digit jumps, keeping in mind that ancestral species can have as many digits as extant species, until you reach a single ancestral species which is common to all extant species; just be sure to indicate digit number at every node.) [PEEK]
    12. Name two taxa that a phylogenetic classification scheme might include with the reptiles but a phenotypic classification scheme (i.e., that typically employed) does not. [PEEK]
    13. What is a cladogram? [PEEK]
    14. True or false, ideally, taxonomic nomenclature provides phylogenetic information. (circle one correct answer) [PEEK]
  29. Practice question answers
    1. Phenotypic classification concerns the classification of organisms by how they look whereas phylogenetic classification is specifically concerned only with evolutionary relationships. Phenotypic classifications can result in polyphyletic taxa (e.g., the protists or monera which are both based on the superficial resemblance of unicellularity or non-eucaryotic cellularity) whereas phylogenetic classification is concerned particularly with creating monophyletic taxa (e.g., archaeobacteria).
    2. below:
    3. Eukarya     ---   Domain     
      Animalia    ---   Kingdom    
      Chordata    ---   Phylum     
      Vertebrata  ---   Subphylum  
      Mammalia    ---   Class      
      Primates    ---   Order      
      Hominoidea  ---   Superfamily
      Hominidae   ---   Family     
      Homo        ---   Genus      
      Sapiens     ---   Species    
    4. below:
    5. below:
    6. Eukarya     ---   nucleated cells            
      Animalia    ---   animals                    
      Chordata    ---   notochord containing       
      Vertebrata  ---   spinal chord containing    
      Mammalia    ---   hair and breasts           
      Primates    ---   nails, grasping digits, etc.
      Hominoidea  ---   apes and humans            
      Hominidae   ---   bipedal apes               
    7. Common ancestry.
    8. Phylum, order, genus.
    9. phenotypic or phenetic.
    10. G(E(A,B),F(C,D)) where parenthesis denote descendant species. Circle all but, for example, A and you have a paraphyletic taxon (i.e., one missing at least one descendant species, i.e., A.
    11. below:
    12. birds and mammals
    13. A graphical representation of a phylogeny.
    14. True.
  30. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. ???-???.
    2. Campbell, N.A. (1996). Biology. Fourth Edition. Benjamin/Cummings Pub. Co. Menlo Park, CA. p. 542.
    3. Li, W-.H., Graur, D. (1991). Fundamentals of Molecular Evolution. Sinauer Ass., Inc., Pub. Sunderland, Massachusetts. pp. 118-119.
    4. Milstein, M. (1995) A glimpse of early life forms. Science 270:226.
    5. Postlethwait, J.H. and Hopson, J.L. (1995). The Nature of Life. Third Edition. McGraw-Hill, Inc. New York. pp. 433-441.
    6. Prescott, L.M., Harley, J.P., Klein, D.A. (1996). Microbiology. Third Edition. Wm. C. Brown Pub. Dubuque, Iowa. pp. 390-414.
    7. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 560-572.
    8. Raven, P. H., Johnson, G. B. (1996). Biology. Fourth Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 634-648.
    9. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 250-255.