Laboratory Notes for BIO 1016 & 3001

© 8 February 2013, John H. Wahlert & Donald McClelland


Classification I—What is it?


Taxon (plural taxa): The formal name of a monophyletic group of organisms (Sciurus is the genus level taxon that includes all species of squirrel that shared a common ancestor and are thus a monophyletic group)
Taxonomic level: the rank of a taxon in a hierarchical classification.  Domain, Kingdom, …, Genus, etc., are taxonomic levels.
Taxonomy: The theory and practice of classifying organisms.  Identifying species, grouping similar species into genera, etc., are a part of taxonomy.

Species:  We will use the textbook definition the biological species: “A population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but do not produce viable fertile offspring with members of other such groups” (Reece et al., 2011: G-33).  A species is thus reproductively isolated from other species; there is no gene flow between them.  Read the section on “The Biological Species Concept” in the textbook for more detail.  Note that three other species concepts are described: morphological, ecological, and phylogenetic.  The species concept one uses depends on the organisms of study.  Imagine you study bacteria that reproduce asexually or that you are a paleontologist who studies long-dead organisms; the biological species concept would not apply.

Note:  Please keep a dictionary handy (print or online), and look up any words that are unclear to you.  Be aware that some words have specific meanings in biology that are different from common usage. Definitions of taxon,

What is classification?

Classification is assigning things to categories.  Categories are concepts that include objects with features in common.  We use categories to organize and simplify our perception of the world, and, as a society, we agree on categories and on the characteristics of objects that belong to them.  Where can you find this social agreement?  It’s called a dictionary; that’s where I found a simple definition of “classification.”

Think about chairs.  You lump them together in a category and do not memorize each as a different thing.  If you say, “Please bring me a chair,” what do you expect?  Do all chairs look alike?  Does it matter if the person hearing you has the same concept of “chair”?

List some of the features that all chairs have in common (this could be a dictionary definition).


Classification is fundamental.

“Taxonomy [classification] reflects man’s urge to understand the patterns of diversity among organism.  Recognition of repetitive patterns in nature long antidates the origin of our own species, as should be clear to anyone who has watched a grazing or hunting animal.  Conscious thought about those patters, and efforts to organize a hierarchial scheme of classification, may be more specifically human characteristics.  Such thought and efforts have roots deep in our evolutionary and social history.  People in primitive, nonliterate societies the world over recognize and have names for the kinds of plants and animals that are significant to them, and at least a rudimentary classification of these basic kinds into larger groups.” (Cronquist, 1988: 1)

“The discontinuous distribution of diversity in nature is evident to any thoughtful person.  In an oversimplified metaphor, one might take the particular combination of characters of an individual organism to be a point on an immense chart.  Points for different individuals may be entered at various positions on the chart, according to their degree of similarity and difference.  When these points have been recorded for enough organisms, it will be seen that they are not randomly distributed.  Instead there are clusters of all sizes and degrees of density and complexity, separated by open spaces of greater or lesser size in which there are few or no such points.  A great many combinations of characters that one might imagine simply do not exist.  There are no photosynthetic dogs, and probably no purple cows.  Neither do we get figs from thistles.” (Cronquist, 1988: 1)

Biological Classification:  How many organisms are there to be classified?

Classification is necessary for understanding the world of organisms because there are so many organisms.  E. O. Wilson (1992:132-133) estimated the number of known species of organisms (plants, animals, fungi, bacteria, protists) to be about 1.4 million.  At the rate new living species are being discovered, this is probably less than a tenth of the number that live on the earth today.  If you add to this the extinct species that populated the world over the past billions of years, the sum is so large that it seems almost infinite.

Although classification itself can be traced back to the earliest written records, the works of Carl Linnaeus (1707-1778) are taken as the starting point for modern classification of animals (Systema Natura, 10th Edition, 1758: and of plants (Species Plantarum, 1753: Vol I:; Vol. II:

Linnaeus lived at a time when explorers were bringing back to Europe specimens and information about heretofore unknown and little-known parts of the world.  Many of the plants and animals were new to the people who studied nature.  Knowing the few hundreds of animals and plants in one’s neighborhood was no longer a complete picture of the world.  Linnaeus was one among many Europeans studying the plants and animals, and he was instrumental in bringing order to the jumble of new specimens.  He was a keen observer of detail and dissected specimens, including flowers, under the microscope.

“For Linnaeus the naming and ordering of the products of Creation linked the study of nature with the worship of God.  Linnaeus’s conception of order reflected his vision of creation as a balanced and harmonious system.  Classification, he thought, could reflect that harmony.  In his later writings Linnaeus also described a general balance of nature.  Every plant and animal fills a particular place in the network of life and helps maintain that network.  Carnivores, he observed, daily destroy animals that if unchecked, would reproduce so quickly as to outstrip their sources of food.  Such intricate relationships offered proof of a divinely sanctioned balance.”  (Farber, 2000: 11)

Linnaeus wrote: “The first step in wisdom is to know the things themselves; this notion consists in having a true idea of the objects; objects are distinguished and known by classifying them methodically and giving them appropriate names.  Therefore classification and name-giving will be the foundation of our science” (1735: p. 9, transl.)

Biological nomenclature is binomial (two names designate a species).

If you examine the Systema Natura, you will notice first that the entire book is in Latin, which was the language of science in Linnaeus’s time.  Before Linnaeus, there was no one standard for naming organisms, and the series of adjectives modifying a noun (fluffy, brown, growly, small dog) could be long; how much of it was the name of the organism?  Linnaeus limited the name of a species to two parts, the Genus, which is capitalized, and the descriptive species name in lower case.  To set the name apart from the rest of the text in Latin, the name was underlined or italicized.  For example, humans are Homo sapiens; homo is the Latin word for man, sapiens is a Latin word meaning wise.  There are other species of Homo, but they are extinct (perhaps they weren’t as wise).  The binomial name must be unique; no other organism may have the same binomial name.  The descriptive species name can be used in other genera (by itself, it is not unique).  Thus species are always referred to with the binomial and, by another rule, in the Latin alphabet (even if the paper is in Chinese).

Who says?
There is worldwide social agreement on this naming convention:
International Code of Zoological Nomenclature:
International Code of Botanical Nomenclature:

Quoting from the International Code of Zoological Nomenclature:

  • Article 5.1. “Names of species. The scientific name of a species, and not of a taxon of any other rank, is a combination of two names (a binomen), the first being the generic name and the second being the specific name. The generic name must begin with an upper-case letter and the specific name must begin with a lower-case letter [Art. 28].
  • Article 11.2 (in part). Mandatory use of Latin alphabet. A scientific name must, when first published, have been spelled only in the 26 letters of the Latin alphabet (taken to include the letters j, k, w and y)…
  • Underlining or italics are not a rule but a recommendation:  “The genus and species name are conventionally written in italics (or more rarely another contrasting typeface) to distinguish the name from surrounding text. This is desirable and recommended, although not mandatory (Appendix B6).”

Why can’t I call a squirrel a squirrel?
In science Sciurus refers to the same genus everywhere without ambiguity.  Squirrel is an English word.  Try it out in France (écureuil), Germany (Eichhörnchen), Slovakia (veverica), China (松 鼠 sōngshŭ), and people will say their native equivalent of “huh?”  For fun, look at a web site where you can “learn to say ‘squirrel’ in almost 300 languages”

Even within a country, common names may be local, and the same name can refer to something different in a different place.  For example, consider the common name “gopher,” what you get depends on where you are in North America:

  • A burrowing rodent (family Geomyidae) with fur-lined pouches on the outside of the cheeks, found in North and Central America.
  • Any of several ground squirrels (rodent family Sciruidae) of the genus Citellus, of the prairie regions of North America.
  • A tortoise (Gopherus polyphemus, family Testudinidae) of dry sandy regions that excavates tunnels as shelter from the sun, native to the southern US.

Hierarchy is an important aspect of classifications.

Hierarchies are necessary to organize and retrieve information. When there are too many things to remember individually, we rely on hierarchies to simplify our daily lives.

  • Consider the supermarket: in the cereal section; here you will find cold cereals and, next to them, hot cereals.  You would be very surprised to see a chunk of meat in the middle of the cereals.  Imagine how long it would take to shop, if supermarket products were not organized by category.
  • When you look for a book in the library stacks, you are guided by the call number of the book you want. Shelved next to it are other books on the same subject.  The call numbers are a hierarchy of sets.
  • For many, the library as a resource has been replaced by the internet.  When you search online, the terms you enter define a set to which the pages found should belong.  You use a mental, intuitive classification.  Often you have to refine a search, e.g., “dogs” would be too big a category if you want to learn about how dogs move; you might refine your search by entering +dog  +locomotion.  When you scan the brief description of each page, you open some and reject others; you reject the pages that are obviously off target and thus mistakes.

Classification usually is hierarchical, that is, it has levels of organization—one big set may have smaller sets nested inside it.  For example, “Please bring me a seat” is different from “Please bring me a chair.”  A seat could be a sofa, a stool, a bench, or a chair.  “Seat” is a concept for a set of objects that includes “chair.”

Where would the term “furniture” fall within this hierarchy?

Draw a hierarchy of nested circles to show the sets for furniture, table, seat, chair, sofa, etc.



Hierarchy has special terms (taxonomic levels) in biological classification.

Linnaeus recognized about 4,400 species of animals and organized them into five hierarchical levels of classification.  The five hierarchical levels, each followed by a description of its characteristics, are:

Regnum (=Kingdom) Animale
Classis (=Class) I – VI: Mammalia, Aves, Amphibia, Pisces, Insecta, Vermes
Ordines (=Order), Mammalia I – VIII: Primates, Bruta, Ferae, Bestiae, Glires, Pecora, Belluae, Cete,
Generum (=Genus)
Species (listed under each genus)

You will find more taxonomic levels of classification in the laboratory manual, and these are updated to reflect the classification used in the textbook.  These and many more additional levels accommodate the huge richness of species discovered since Linnaeus’s time.

      Phylum or Division

McKenna and Bell (1997) classified more than 5000 fossil and living mammalian taxa assigned to generic or subgeneric (between genus and species) rank and used 25 taxonomic levels to arrange them.  This number is greater than Linnaeus’ total for all animals.

Click here for a classification of the groups we will study in the laboartory.


  • Cronquist, A.  1988.  The Evolution and Classification of Flowering Plants.  Second Edition. The New York Botanical Garden Press. Bronx, NY.
  • Farber, P. L.  2000.  Finding Order in Nature.  Baltimore, Johns Hopkins University Press.  136 pp.
  • Linnaeus, C.  1735.  Systema Naturae, facsimile of the first edition, with an introduction and a first English translation of the "Observations," by M. S. J. Engel-Ledeboer and H. Engel, Nieuwkoop, Holland: B. de Graaf, 1964; 30 pp.
  • McKenna, M. C., and S. K. Bell.  1997.  Classification of Mammals Above the Species Level.  New York, Columbia Univ. Pr.  631 pp.
  • Reece, et al.  2011.  Campbell Biology, Ninth Ed.  New York, Benjamin Cummings.  1263 pp, and additional sections.
  • Wilson, E. O.  1992.  The Diversity of Life.  Cambridge, The Belknap Press of Harvard University Press.  424 pp.

Web resources on Carl Linnaeus:


Classification II—What does it mean?

How do I decide what goes with what?

Objects with features in common are placed together in a group.  In the supermarket cereal example, there could be subgroups of oat cereals, wheat cereals, and rice cereals.  Linnaeus used the male and female reproductive structures of plants as the basis for comparison in his botanical classification.  For animals, he used a diversity of structures to form taxonomic groups and was the first to consider the teeth in quadrupeds.  He coined the term Mammalia for animals with mammary glands that suckle their young.

The simplest approach, which you can follow in the laboratory set up with skeletons, is to move the specimens around, put them side-by-side, and assess what is similar and different about them.  Then, you put into words what you see—the describable features—the characters and the different states for each character.  Here is an example:





character states

character states

flight membrane



support of flight membrane



The composite description of many character states allows one taxon to be distinguished from another.  Someone else can look at a specimen, read your description of character states, and decide if the specimen is the same kind of organism you were looking at.  The character state descriptions and pictures in field guides to birds are designed to help you identify different species.

Analogy:  Birds and bats both fly but they are so different that they are not classified in the same group.  That is because their wings, which serve the same function, are built very differently.  This is an example of analogy:  “A part or organ in one animal which has the same function as another part or organ in a different animal” (Owen, quoted in Boyden, 1943).  The bat and bird wings are said to be analogous.

Homology:  If you look at the bones that make up the two structures, you will find a series that matches your own arm: shoulder blade, single upper arm bone, pair of lower arm bones, wrist, and hand (very different in bird and bat).  The structural correlation is homology:  “The same organ in different animals under every variety of form and function” (Owen, quoted in Boyden, 1943).  Homology and analogy are different qualities that are not dependent on each other.

Boyden (1943: 230) quoted additional statements by Owen that expand on the concept of homology and tell how to recognize it:  “These relationships [that is, homologies] are mainly, if not wholly, determined by the relative position and connection of the parts, and may exist independently of form, proportion, substance, function, and similarity of development.  (1848, p. 6)”  “’Homological anatomy’ seeks in the characters of an organ and part those, chiefly of relative position and connections, that guide to a conclusion manifested by applying the same name to such part or organ… (1866, p vii.)”

The conclusion that the bones of the bat wing, bird wing, and human arm are homologous is based on the relative position and connection of the bones to each other.  To apply the arm bone names, humerus, radius, ulna, etc., to the elements of a bird wing, bat wing, and human arm is to state that they are homologous.  Owen (quoted by Rupke: 120) viewed homologies in vertebrates as modifications of an archetype, which he described as “that ideal original or fundamental pattern on which a natural group of animals or system of organs has been constructed, and to modifications of which the various forms of such animals or organs maybe referred.”  His archetype resembled the creature we know as amphioxus.

“The modern formulation of the criteria for recognizing homology are frequently attributed to Remane (1952), and can be stated as follows(Schuh, 2000: 64):

  1. position (similarity of topographical relationships)
  2. similarity of special structure
  3. connection by intermediates (transformation)”

Darwin gave homology and thus classification a new meaning.

Darwin reinterpreted the anatomical evidence.  To him, homologies suggest that their possessors shared a common ancestor, which already had these characters.  This assumes a heritable or genetic basis for the characters.  Thus organisms that are classified together are each other’s closest relatives.

“All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike”  (Darwin, 1859: 420).

Analysis of homology became the basis for proposing common ancestry and a phylogeny—a hypothesis of the evolutionary history of a species or group of related species.  The hypothesis of what happened in the past is often represented as a phylogenetic branching diagram (cladogram) or tree that shows how species and groups of species are thought to be related to one another.

Contemporary biological classifications aim to show relationships by reducing the phylogenetic hypothesis to a series of nested sets.  Many textbooks say that common ancestry is the ultimate test of homology.  This is nonsense since the hypothesis of ancestry is based on analysis of homology.  What a phylogeny can reveal is that some supposed homologies do not fit and are human errors in assessing characters—perhaps they arose independently and were not present in a common ancestor.


  • Boyden, A.  1943.  “Homology and analogy: a century after the definitions of ’homologue’ and ‘analogue’ of Richard Owen.”  The Quarterly Review of Biology, 18:228-241.
  • Darwin, C. R.  1859 . On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. [1st edition]
  • Darwin online:
  • Rupke, N.  2009.  Richard Owen: Biology without Darwin, a Revised Edition.  Chicago, Univ. Chicago Pr.  344 pp.
  • Schuh, R. T.  2000.  Biological Systematics: Principles and Applications.  Ithaca, Comstock Publ., Assoc.  236 pp.


Classification III—How is it done?

Vocabulary (Modified from Schuh, 2000, glossary):

Apomorphic character-advanced/derived, as opposed to primitive or plesiomorphic
Apormorphy-an advanced/derived character; a group-defining character
Synapomorphy-shared, advanced/derived, group-defining character
Autapomorphy-an advanced/derived character that is unique to a taxon
Plesiomorphic character-primitive, as opposed to advanced/derived; the quality of being group-defining only at a higher level
Plesiomorphy-a primitive character, not group defining at the level at which it is being observed; the quality of being primitive
Symplesiomorphy-shared, primitive characters defining groups only at higher levels
Homoplasy-error in homology assessment (sometimes irreparable)

Using homology to speculate on relationships

We use statements of homology to reconstruct the evolutionary histories of organisms.  Initially, we hypothesize that if a certain feature (character/character state) appears to be the same in different organisms it is homologous since this is the most parsimonious or simplest explanation.  Such hypotheses are statements of primary homology.  With enough data like this, we can reconstruct the evolutionary history of a group of organisms.  The characters we use can include morphological features, behaviors, and DNA sequences.  In order to test our hypothesis about homology and build an evolutionary tree, we can conduct a phylogenetic (cladistic) analysis.  Phylogenetic analysis groups species based on shared derived characters, synapomorphies, not on overall similarity.  In a phylogenetic analysis, characters coded in a matrix are used to construct an evolutionary tree—a phylogeny—for the organisms.  This tree represents a hypothesis about the relationships of the organisms.  After the phylogeny is constructed, the characters of the organisms can be optimized, i.e., placed on the tree where they arose or changed.  We can then see how many times a character evolved, if it has a single origin or if it is homoplasious (multiple origins).  This is secondary homology.  Once homoplasy is indicated, we can reexamine how the characters were coded; perhaps, we made a mistake in our assessment of primary homology and we see differences that were overlooked.

Back to our example of flight:  Suppose we decided to use flight as a character in a phylogenetic analysis.  To code flight as a character we need to break it into discrete character states.  Often presence/absence characters are used.  In our flight example, the character could be “flight” (i.e. ability to fly) and the character states: absent 0 (i.e. organism unable to fly); present 1 (i.e. organism able to fly).  This would be a primary statement of homology, and we would be hypothesizing that flight was homologous.  If we coded flight along with other characters we could end up with a matrix like this.  (Note: This is only a small, sample matrix.) 


absent 0; present 1

absent 0; present 1

Mammary glands
absent 0; present 1

simple 0; compound 1




































If we analyzed this matrix (with more characters), and optimized the character flight onto the resulting phylogeny, we would see that ability to fly is actually homoplasious, having evolved separately in bat, birds, and insects.  Let’s reexamine our primary assessment of homology for flight.  Did we make a mistake in the assessment?  Clearly, we can see that the methods by which insects, birds, and bats, fly is quite different; therefore, our initial hypothesis of flight being a homologous character within animals was wrong.  The process of reexamining characters in light of a phylogeny is called reciprocal illumination.  Reciprocal illumination is not circular logic; it is simply checking for and correcting errors.  There is no reason to believe that we were infallible in our original assessments, and it would be ridiculous not to correct errors.  However, if we found that there really was no other way to assess one of our characters, we would simply consider the character homoplasious and leave it at that.  Keep in mind, a homoplasious character can still be a synapomorphy for specific groups.  For example, presence of stellate hairs in the plant genus Solanum (Solanaceae) is a synapomorphy for Solanum subgenus Leptostemonum even though stellate hairs are found in other groups of plants.

Though we often use presence/absence characters, we can also use more complex character coding.  For example, we might have a set of plant species with different flower colors; some  yellow, some red, and some white.  We could code this character as “petal color” and the characters states “yellow 0”, “red 1”, and “white 2.”  If we ran an analysis with the flower color character in our matrix, we might find that there are two instances of the evolution of red petals.  In this case red petals would be homoplasious.  If we used reciprocal illumination we might find that different pigments (e.g. anthocyanins vs betalains) were responsible for the red colors of the different species.  We could then recode the character to distinguish between red petals from anthocyanins and red petals from betalains and analyze the matrix again.

Making classification reflect evolutionary history.

One of the most valuable aspects of classification is its predictive value. For example, by knowing the scientific name of a species, the user automatically knows many things about that species including many morphological and chemical characters.

In order to confer this predictive value onto a system of classification, the system needs to reflect the evolutionary history of the included organisms. For this reason we recognize monophyletic groups rather than paraphyletic or polyphyletic groups. A monophyletic group is a group containing a hypothetical common ancestor and all of its descendants. Since a monophyletic group reflects the evolutionary history of the organisms, it is said to be a natural group. A paraphyletic group contains a hypothetical common ancestor to a group of species but does not include all the descendants of that ancestor. A polyphyletic group is a mixture of organisms from different lineages. Both paraphyletic and polyphyletic groups are not natural. In the illustration below you can see that the group formed by taxa A, B, and C form a monophyletic group. The group formed by B and C is paraphyletic, and the group formed by A, B, and D is polyphyletic.


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Last updated 24 feb 2013 jhw