Classification. Note: At some point in your biological education, you have probably read something like this before. So I suggest that you speed-read this file and then spend your time in more worthwhile endeavors.

An organism’s name is the key that opens the door to everything scientifically known about the creature in question. Thus in any scientific enterprise, an important objective is to name the objects of study, and every animal known to science has a scientific name. The name is always in Latin and is therefore italicized to separate it from the basic language (English, Shona, Portuguese, Vietnamese, whatever) of the text in which the name occurs. The scientific name is almost always taken from the first published, formal description of the animal; usually the name is supposed to mean something in Latin or Latinized Greek.

Initially many students wonder why scientific names are written in Latin, a language spoken by almost nobody today. In part the reasons are historical. In the 1700’s, world travel was becoming more common, and biologists were increasingly confronted by an array of creatures unfamiliar to them—and which did not have names in the biologists’ native languages. Confusion reigned for a time, but at last a Swedish botanist named Carl von Linné (who published under the Latinized name of Carolus Linnaeus) tackled the great task of organization, suggesting a standard name for every known plant and animal. (For animals, the official, standard first list is Linnaeus, C., 1758. Systema Naturae, 10th Edition.) Latin was a good choice of languages for several reasons. First of all, Latin by-passed international jealousies. If Linnaeus had written in Swedish, the Russians would have been irate. If he had selected French, the English and Spanish would have felt insulted. If he had written in Dutch or Chinese, nobody else would have been able to read his work. If he had written in English—well, of course I think he should have catalogued the earth’s biota in English, but most of the world would disagree. Second, Latin was a language that was understood by every educated man in Europe. (At least every educated man in Europe pretended to know Latin. And Linnaeus probably did not care much about the women, the uneducated, or the non-European.) You folks might be interested to know that graduates in Wofford College’s early years were required to prepare valedictory speeches in Latin. I presume that these speeches possessed the virtue of brevity. Third, because Latin is a “dead language,” the meanings and spellings of its words are frozen and do not change through popular use. What latirostris means today, it will also mean tomorrow. Fourth, the advantages of using any common language should be obvious to most folks. (a) A common language solves the many-animals-one-name problem. I study crocodilians, and I have been amused to discover that the term alligator refers to one species here, another in Belize, another in Cameroon, and another in Australia. But the scientific name, Alligator mississippiensis, refers to exactly one species. (b) A common language also solves the many-names-one-animal problem. A secretive aquatic snake from the South Carolina Lowcountry is variously called “rigid watersnake,” “glossy watersnake,” “glossy crayfish snake,” and “that little brownish snake I just raked out of the muck.” For formal communication, I can avoid confusion by using the name Regina rigida. If you ever work in a country where you do not speak the language or where you speak it poorly, you may develop an especial appreciation for Latin, scientific names. When I taught in Ho Chi Minh City, I could pick up a local publication about natural history and recognize

perhaps one Vietnamese word out of twenty. But when I saw the Latin, Crocodylus siamensis, I knew the paper was about the mainland Southeast Asian freshwater crocodile, and I knew that I should find somebody to help me translate. Now that I have written at length in praise of Latinized, scientific names, I should also admit that they have their problems. They are not quite as “standard” as some people might have you believe. When we study frogs, I may tell tales about two herpetologists who came almost to blows over whether spring peepers should be called Hyla crucifer or Pseudacris crucifer. Sometimes the scientific name gives erroneous information about the animal to which it refers. Coluber constrictor is a common North American snake—but it is most definitely not a constrictor! (The original describer of the species believed incorrectly that the snake constricted its prey. And now, because of priority rules, the name must not be changed.) Sometimes scientific names mean almost nothing at all. A biologist describing insects in South America had been aggravated by a particular sort of beetle and decided to name the species Aggra vation. Organisms have been named for children, spouses, lovers, and political patrons. A liberal friend of mine even wanted to give a new species a semi-obscene name in dishonor of President Ronald Reagan. The rules for pronouncing scientific Latin are neither precise nor standardized. I suggest that you simply say the words as if they were written in your language. If someone corrects your pronunciation, you should raise an eyebrow and say, “Well, Roger Conant told me….”

Every animal’s scientific name has at least two parts. Many animals have three-part scientific names, but the first two parts are the most important and will usually be the only ones we consider in this course. (See below.)

a. Part 1 is the genus name. It is always capitalized; occasionally it is abbreviated by its first letter and a period.

b. Part 2 is the species name. It is never capitalized; occasionally it is abbreviated by its first letter and a period.

c. Part 3, if present, is the subspecies name. It is never capitalized or abbreviated, but it is often omitted.

This box begins with a short paragraph that will illustrate the grammatical use of scientific names. After the paragraph I will offer a brief discussion of the grammar. Then I shall write a little more about scientific names in general.

Probably the most common venomous snake in South Carolina is Agkistrodon contortrix, the copperhead. Herpetologists recognize two subspecies of A. controtrix in the State. The Lowcountry and Midlands subspecies, A. c. contortrix, has lighter background color, and its chestnut-colored “hour-glass” crossbands often meet asymmetrically at the mid-dorsal line. The Upcountry subspecies, A. c. mokasen, is darker, and its crossbands are usually more symmetrical.

The first time the genus name (Agkistrodon) is used, it is written out entirely. After that it can be abbreviated so long as confusion with other generic names is unlikely. Agkistrodon contortrix is the full name of the species. If we are not concerned about differentiating between subspecies, we need not add a subspecific name. After we have mentioned the full species name, we can abbreviate both of the first two parts when we also use a subspecific name (hence A. c.

controtrix is appropriate; however, a simple A. c. without any third part would not be acceptable). One subspecies (the first one formally described) will always repeat the species-name—as in Agkistrodon contortrix contortrix. This is sometimes called “the nominate form.” Note that even when a specific (or subspecific) name is derived from a proper noun, it is never capitalized. (Consider, for example, the Carolina anole, Anolis carolinensis.) If you are writing a scientific name by hand (or on an old-fashioned typewriter, if anybody still uses such machines these days), you should not try to imitate italic script but should simply underline the scientific names.

(Warning: This is boring; speed-read the rest of this box.) Often during the semester, my discussions may be full of scientific names. I do not intend for you to memorize these names, but you should record at least a few of them in your passive memory. If you spend any time studying scientific names, you will discover that most generic names are not really Classical Latin words at all. Instead, most of them were formed by Latinizing word-stems, prefixes, and suffixes that were originally Greek. (As I understand the process, “Latinizing” involves two steps. [1] You change the letters from those “weird,” hard to type Greek characters into Roman characters found on most typewriter keyboards. This may also require altering Greek letters with no direct Latin equivalents; for example, Latin has no k, so Greek letters with a k sound are usually rendered as c. [2] You say, “Hey, folks, now this has been Latinized. It’s my choice for a scientific name, and after I publish it, you’re stuck with it.”) A few generic names do have Classical Latin roots; others find their origin in languages of peoples sharing a homeland with the described species. Species names, too, often have their own Greek roots. But, more commonly, they are (1) repetitions of the generic name, (2) Latin adjectives (for such words as big, reddish, aquatic, etc.), (3) names of places (often where the first specimen of a species was secured), or (4) names of people. (Note: Although naming a varmint for yourself has always been considered somewhat tacky, naming it for another biologist was once the fashion. Nowadays most journal editors prefer species-describers to avoid any personal names at all.)

Of course the two-part Latin names cannot suggest any overall organization of biota above the level of the genus, and biologists have consequently erected a set of hierarchical categories. Every genus is a member of a Family. Every Family is a member of an Order. Every Order is a member of a Class. Every Class is a member of a Phylum. And, for animals, every Phylum belongs to the Kingdom Animalia.

It is important for students to remember the order of the hierarchy. Mnemonic devices are sometimes appropriate. During my much younger days at Wofford, I temporarily had a crush (innocent, unfortunately) on a young woman whose initials were K. P. (I shall not give the full name because today this woman is a prestigious biologist in her own right—and she sometimes asks for copies of my lecture notes.) So I immediately thought of the sentence, “K. P. Cries Out For Great Sex.” This takes you from Kingdom to Species, keeping everything in order. Here are a few extra hints for you. Animal Family names are usually long, but all of them end in –idae, which at least makes them easy to recognize. Animal subfamily names end in –inae. Scientists are less formal about names above the Family level. (For example, the name for one Class of interest to us is “the Reptilia.” But nobody can say you are unscientific if you call it “the reptiles,” or “los réptiles,” or whatever.)

There are numerous other levels of classification that are occasionally used. Many of them fall obviously within the K,P,C,O,F,G,S order. Consider, for example, Subclass, Superfamily, and Infraorder. On the other hand, modern cladistic taxonomy requires even more categories, and as you read some recent herpetological literature, you may see references to Granorders, Tribes, Cohorts, and so on. Usually the context makes the meaning clear. In any case, I try not to think about this proliferation of terms too often, and at this point you should probably follow my example. Here is an example of reasonably full reptilian classification. The victim is our old familiar Lowcountry copperhead, Agkistrodon controtrix contortrix: KINGDOM: Animalia. PHYLUM: Chordata. SUBPHYLUM: Vertebrata. CLASS: Reptilia. SUBCLASS: Lepidosauria. ORDER: Squamata. SUBORDER: Scleroglossa (or, to be more old-fashioned, Serpentes). FAMILY: Viperidae. SUBFAMILY: Crotalinae. GENUS: Agkistrodon. SPECIES: contortrix. SUBSPECIES: contortrix. EXPLICATION OF NAME: Ankistron is a Latinized form of a Greek word that (I think) means “fishhook.”; odontos means a tooth. The generic “fishhook-tooth” refers to the snake’s fangs. The specific, contortrix, probably means “one that is able to twist.” One authority suggests that it refers to possibility that you’d contort yourself in pain if one of these cute little snakes bit you. (I would have chosen the name faecesdixit, which gives the Latin for what you’d probably say if a copperhead bit you….) Another author suggests the name refers to the condition of the type specimen. If this really interests you, perhaps you would like to look at the Web site, http://ebeltz.net/herps/etymain.html, which explicates the names for many North American amphibian and reptile species.

The Linnaean system of classification, with its hierarchies, existed for about 100 years before Charles Darwin popularized his ideas on the origin of species by natural selection. Because Linnaeus worked in a pre-Darwinian world, his classification system was necessarily phenetic. (That is, he attempted to address the question, “How similar are two taxa?”) Today, in the strong light of Darwin, most authorities prefer systems that are cladistic. (That is, they address the question, “How closely related are two taxa?”)Thus a cladist thinks of classification-hierarchies this way: If two animals are very, very closely related, they should be placed in the same subspecies. If they are very closely related, they should be placed into the same species. If they are rather closely related, they should be placed into the same genus, and so on.

Consider the problem of defining the branching hierarchy between three taxa: crocodiles, birds, and lizards. Clearly, crocodiles and lizards are most alike in almost any sense you could define. Thus a phenetic system would express their branching order like this (next page):

On the other hand, crocodiles and birds probably share a common ancestor from the mid-Triassic while the common ancestor between [crocodiles + birds] and lizards may be from the Paleozoic. Therefore a cladistic system would express their branching order like this:

Students of mammals might consider phenetic and cladistic “trees” for people, gorillas, and chimpanzees.

This class is not the appropriate venue for formally defining such tricky concepts as “closeness of relationship.” But in non-technical language, “how close two animals are related” means “how long ago two animals shared a common ancestor (box).” Animals that share more recent common ancestors are assumed to be more closely related, even if they do not look very much alike. Throughout this course I shall occasionally address this relatedness-issue within more specific contexts.

The idea of measuring “closeness of relationship” by “recent-ness of ancestry” is reflected in most human kinship systems. You share a more recent common ancestor with your sister than with your cousin. (For the former, the most recent common ancestor would be your parents; for the latter it would be your grandparents.)

In the absence of a definite fossil trajectory with clearly attributable ancestors (and such trajectories are exceedingly rare), closeness of relationship is estimated by analyzing taxonomic characters (e.g., number of toes, color of scales, presence of palatine teeth, nucleotide sequence of cytochrome b…). Some such characters can be informative, and some can be uninformative. I’ll give examples in a table below—and also provide the fancy names by which the taxonomists label the character-types. The three organisms evaluated will be the American Alligator (“gator”), the Solomon Islands Giant Prehensile-tailed Skink (“lizard”) and the Bobwhite Quail (“bird”):

Character States: Character Type: Informative? Why?Gator, lizard, and bird all have 4 limbs.

Uniform symplesiomorphic(The italicized word means “ancestral, shared”)

NotInformative.(I.e., it doesn’t help us decide who’s related to whom.)

Since all the varmints have the same character-state, this character is useless in trying to decide which species-pair is most closely related.

Gator and bird lay eggs.

This lizard does not (though most lizards do).

Variant symplesiomorphic(“ancestral, shared”)

Not informative.

Because “analysis” of the character would lead us to the correct conclusion, it may seem informative. But by formal logic, this situation is identical to the two that follow—and each of those would lead us to the wrong conclusion.

Gator and lizard both have teeth. The bird does not.

Variantsymplesiomorphic(“ancestral, shared”)

Not informative.

Both the lizard and gator retain a feature shared by their shared ancestor—and by the shared ancestor of birds. This trait persisted in the gator-bird lineage but was lost fairly recently in birds’ flight-specializations.

Bird and lizard are both terrestrial. Gator is aquatic.

Variant symplesiomorphic(“ancestral, shared”)

Not informative.

Both the lizard and the bird retain a feature shared by their common ancestor—and by the shared ancestor of gators. The trait persisted for a time in the gator-bird lineage but was eventually lost by the gator.

Bird and lizard eat vegetable matter.

The gator does not.

Variantconvergent(means “similar character separately evolved in separate lineages”)

Not informative.

All three taxa are descended from a meat-eating common ancestor. The lizard and bird evolved herbivory separately, as part of their two different responses to environment.

In gator and bird, choanae (funnel-like tubes of nasal cavity) are curved posteromedially.

In lizards they are not.

Synapomorphic (means “derived, shared”)

Informative. The gator-bird-lizard common ancestor had choanae not curved posteriomedially. The lizard retained that condition, but at some point a varmint in the gator-bird line evolved choanae curved posteromedially. The presumption of this shared-derived ancestral condition causes the bird and gator to be classified together.

Of course it is not always easy to say what characters are synapomorphic—and are therefore informative to the taxonomist. Consider, for example, the fact that gator and bird have 4-chambered hearts—while lizard does not. I strongly suspect that this condition is shared-derived (synapomorphic) and therefore informative, but on this score the fossil record is obviously silent. There is no final solution to this problem of recognizing synapomorphies. Therefore, in fact, taxonomists examine large suites of characters across a large number of taxa. Evolutionarily independent clusters of co-varying characters are usually assumed to designate ancestral conditions because this is the simplest way to define the character-types. (This overall strategy is called parsimony; see below.) In some respects the easiest way to gather information on large suites of characters is to analyze genetic sequences (box), and we’ll occasionally talk a little about that in class.

Why Use Genetic-Sequence Data?

1. Estimates of phylogeny have already been established by analysis of anatomical (etc.) characters. Molecular data allow an independent way to establish estimates of phylogeny. If the two, independent, estimates are similar, then perhaps the joint estimate is pretty good.

2. Genetic-sequence data can provide a vast number of characters to analyze. (For example, the typical terrestrial vertebrate has on the order of 200 bones—and on the order of 2+ billion nucleotide pairs. In fact, the typical modern anatomical taxonomic investigation considers about 100 characters, and the typical molecular taxonomic investigation considers about 1000 characters.)

3. To some degree the patterns of molecular evolution are well understood. For instance, in most taxa transitions (e.g., A G) are slightly more common than transversions (A T), even though more transversions are possible. (If you’ve forgotten this stuff, you can see an attachment at end of this document.) Mutations in the third position of a codon are more common than mutations in the first or second position. In statistical analyses, such differences can be weighted according to a reasonable, explicit theory of expected frequencies. (That is, genetic theory tells us that a second-position change is more “weighty” than a third-position change. By contrast, there is no general theory that tells us whether the loss of a finger is more significant, taxonomically, than the loss of a toe.)

4. Non-coding regions (“junk DNA”) are by definition transparent to natural selection and are therefore immune to the problem of convergence.

If you are especially interested in this business of taxonomy, particularly as it may be applied in a genetic-sequencing context, then you might click on the following link (which, if I’m lucky, will even work):

Notes on Parsimony Analysis

Please see also Figure 1.2 in Pianka and Vitt.

One of the goals of most modern taxonomists is to define “trees” all of whose branches are monophyletic. This means that each branch should include the branch-groups’ common ancestor—and all of that ancestor’s descendents. Polyphyletic trees are said to be downright bad, and paraphyletic trees are said to be somewhat deceptive. Unresolved trichotomies (or, worse, unresolved polytotomies) are said to be less than ideal. Next I’ll give examples (at least hypothetical) of such weirdnesses.

First, let’s begin with polyphyly, the worst case. At one time the African molevipers (wonderful critters if you want to learn modesty through pain) were placed in the same Family with the true vipers—because both groups possessed long, hollow, folding front fangs. Nowadays it is known that these fangs are convergent characters, evolved along entirely separate evolutionary trajectories and not indicative of any shared common ancestor. (A non-herpetological example—quite obvious, though perhaps a bit silly—would be a taxonomic system that classified tuna and porpoises together, to the exclusion of other mammals.) That is a polyphyletic classification because the (bad) node with molevipers and true vipers includes endpoints of two separate lineages.

Now let’s think about paraphyletic trees. That is a tree on which a node includes a common ancestor and some of its descendents—but not all of its descendents. Consider the following:

In order to include within a group all the varmints we commonly consider “reptiles,” you have to name the group starting at about the point labeled “R,” because that’s on the branch that includes a common ancestor to all the reptiles. If you exclude the blue portions (the Birds) from the Reptilia, then you make the Reptilia a paraphyletic group—because along with (other) reptiles, the birds are descended from common-ancestor R. Note that we often have to (or even choose to) live with paraphyletic trees. For example, in this course I shall offer only scant mention to the most successful reptiles, the birds. And everybody thinks that’s just fine. Sometimes we have strongly suggestive evidence that a group is paraphyletic, but we don’t know exactly how or with what members

properly placed in which groups. For example, that is a taxonomic problem for folks dealing with Asian pond turtles, New World pond turtles, and tortoises. A paraphyletic tree is said to be somewhat deceptive because it can hide evolutionary histories. (E.g., to define reptiles without birds obscures the well-established fact that birds and crocodilians diverged from a common ancestor.)

Now, as a final taxonomic flourish, let us consider unresolved trichotomies (and higher-order unresolved relationships). These are really simple to understand and really simple to recognize on a phylogenetic tree (see below). Unfortunately, in practice they are very difficult to resolve (duh; otherwise they would not remain “unresolved”; sorry, but I’m getting tired). From top to bottom the three snake Families represented on the following tree are (1) the “true” vipers and the pitvipers, (2) the noble molevipers, (3) the advanced, mostly harmless snakes, and (4) the cobras, coral snakes, kraits, mambas, etc.

OK, that tree should be trivial to understand. Amongst the snakes, the Viperidae diverged from a lineage leading to the Atractaspididae, Colubridae, and Elapidae. But nobody (except probably Bernie Dunlap, who knows everything but keeps some things to himself) knows the branching order among the last three Families. If we looked at frogs, we’d find about a dozen Families of unknown branching-order within a group called the Bufoidea. This would be called an unresolved polytotomy (or something of the sort; I may have put in an extra “t”) by people who care for such words.

I would not want to argue that classification is the most important or the most interesting topic that we will study this semester. On the other hand, the concepts I have presented in these notes underlie the vocabulary that we must share in order to communicate effectively about the evolution and natural history of amphibians and reptiles.

Attachment: Transitional substitutions and Transversional Substitutions