The naming of animals (and other life) is known as taxonomy.
What is the problem?
For many students of biology the scientific naming system seems burdensome. Why learn Panthera tigris when there is already a name for this animal, the tiger? However, to discuss animals we must have clear and unambiguous names. While “tiger” is clear enough in English it is only clear in English. For other species the problem is much worse. For instance, the word “panther” currently refers to any of three species. Some members of the species Puma concolor are called panthers, although others are called cougars, mountain lions, mountain devils, catamounts, or pumas. As another example, both leopards (Panthera pardus) and jaguars (Panthera onca) come in two color phases. One phase has black rosettes (hollow spots with broken borders) against a yellowish or tan background. The other is black all over, although under the right light the dark the rosettes are still visible. The black phases of both species are called panthers, although the other phase is not. To make matters worse, the English word panther once simply meant “large cat”, and in older documents is used for any large cat. However, despite this trouble with common names, the scientific Puma concolor, Panthera pardus, and Panthera onca are unambiguous.
This is the problem with common names. An animal may have multiple common names (like Puma concolor) or one name may indicate multiple species (like “panther”). Common names are also common to only one language. “Lion” may clearly indicate a single species in English but the word means nothing in most other languages. A few more examples follow:
- The wolf Canis lupus is known as the wolf, the timber wolf, and the gray wolf. The common names indicate two or three species but there is only one.
- The fish sold as “common plecos” in pet stores may be Hypostomus plecostomus or any of several species of Pterygoplichthys. One name, multiple species.
- The term “shark catfish” includes Ariopsis seemanni, a sea catfish from rivers and near-shore marine environments, every member of the family Pangasiidae (the group is known as the shark catfishes, although only some species have “shark catfish” in their name), and Wallago attu, a large, long-bodied, sharp-toothed catfish from South Asia. The common name indicates that these are one species or at least related but they are unrelated members of the extremely large catfish order.
The Linnean solution
Carl Linnaeus, living in the 1700s, was a botanist who faced difficulties because of this problem with common names. Without a single, unified way to refer to a plant without ambiguity Linnaeus could not be sure that another scientist would correctly understand what plant he was referring to. This was especially problematic because as a Swedish scientist Linnaeus corresponded with scientists all across Europe, each of whom knew plants by different names in different languages.
Linnaeus was not the first person to attempt to solve this problem but he was the one who succeeded. Under Linnaeus’ system a species was given a name formed from two words. Linnaeus tended to use Latin and Greek, the two languages all educated people could be expected to read, in his names. This has led to some people referring to the scientific name of a species as its Latin name. Linnaeus also described each species when he named it, publishing a huge set of books called Systema Naturae. These books gave a name and a description for each species, making it possible for other scientists to use these names without wondering what they referred to.
In many ways it is likely that Systema Naturae was what caused Linnaeus’ system to succeed where others had failed. Originally Systema Naturae included only plants but Linnaeus added animals in later volumes, and the sheer number of species he named meant that another scientist could find a name for a species in Linnaeus’ work and refer other scientists to Systema Naturae for the description. Systema Naturae was actually continued after Linnaeus’ death, but eventually the huge number of species being named proved too much to keep in one volume of books. More recently, with the Internet and computer technology, the idea of a database of all names has come back.
Linnaeus also created a system of nesting groups in which species were organized into a number of levels. This will be covered later in this chapter, but the first of these levels is the genus (plural genera). A genus is composed of closely-related species.
The Modern Linnaean System
Linnaeus’ system works as well as it does in large part because it is so old. Linnaeus’ original system had many issues but debates in the past have led to rules that have solved many of these problems. One strength of the system is that it is a formal system. Originally Linnaeus named everything and kept his own rules. Nowadays an organization called the International Commission on Zoological Nomenclature (ICZN) keeps rules for naming animals (a parallel body, the International Commission on Botanical Nomenclature, keeps the rules for plants). This body has the power to issue ruling solving issues with names. For instance, Linnaeus himself created the genus Simia to contain the monkeys and apes. However, several of the species described within Simia were described in a confused manner. (Specifically, Linnaeus appears to have mixed chimpanzee and orangutan descriptions together in his original description of Simia satyrus.) In Opinion 114 the ICZN voted to suppress Simia and Pithecus on the grounds that both names were unclear and that new, clearer names should be used.
The modern system has a very long set of rules published by the ICZN. Several of these rules are generally important for biologists of all stripes to understand.
- Scientific names are composed of the animal’s genus and a second word, the specific epithet. Confusingly, the species name can mean either the whole name (e.g., Canis lupus) or the second part only (e.g., lupus). If the animal is placed into a new genus the first part of the name will change and the second may change to match the gender of the genus. In Latin and Greek words have gender, and so a Latin or Greek genus name has a gender that the species name has to match. This only changes the end of the word but it can be confusing. For instance, the American bullfrog was originally described as Rana catesbeiana but later moved to the genus Lithobates. This made it Lithobates catesbeianus.
- Groups of species, like genera, are anchored on a specific species. For instance, the genus Silurus is anchored on the Wels catfish, Silurus glanis. Linnaeus placed almost every catfish into Silurus, but later work split the catfish into many genera (and, in fact, many larger groups as well). Because Silurus is anchored on Silurus glanis the group that includes Silurus glanis will always be Silurus and the other groups will get new names.
- The principle of priority. If two scientists name the same species the name that is published first is the one that sticks. This lasts even if the species “disappears”. Brontosaurus excelsus was named in 1879 by Othniel Charles Marsh. It was later decided that Brontosaurus excelsus was in the same genus as Apatosaurus ajax, which Marsh had named in 1877. The principle of priority meant that Marsh’s Brontosaurus was replaced by Marsh’s Apatosaurus. However, in 2015 Tschopp et al. published a study of the Diplodocidae in which they found that the animal first named Brontosaurus excelsus was not actually very closely related to Apatosaurus ajax. Tschopp et al. did not get to choose a new name for this dinosaur since it had already been named once, and so even though the name had not been in use for decades Tschopp et al. called this animal Brontosaurus excelsus.
- Type specimens. In modern times when a species is described a specimen of that species is stored in a museum and designated as the type specimen. This specimen is, by definition, part of that species. For instance, all African elephants were originally named Loxodonta africana. When they were split into Loxodonta africana and Loxodonta cyclotis the type specimen was consulted. The species that the type specimen was remained Loxodonta africana and the other species got a new name.
Scientific Name Style
Scientific names always follow a particular style. Recognizing this style is important. For instance, you may not know what Kryptopterus vitreolus is but if you can recognize the style you know that this is the name of a species.
Presumably, given the number of scientific names in this chapter, you have already deduced the style for a scientific name but the rules are simple. The genus name is always capitalized and the specific epithet never is. The scientific name is always italicized opposite to the text.
The name of the groundhog is Marmota monax
The name of the groundhog is Marmota monax
It is also often common for genus names to be abbreviated after first use. For instance, Canis lupus will be called C. lupus later. C. latrans is Canis latrans. Sometimes, when a single letter is not sufficient (for example, the author has mentioned two genera that start with “C”) a second letter will be used.
Levels Above Species
Linnaeus not only named species, he also organized them into larger categories. For instance, all animals were placed into the Kingdom Animalia. Since Linnaeus’ time some levels have been added. The current system starts with Domains and then goes Kingdom, Phylum (plural phyla), Class, Order, Genus, and Species. Knowing this order is important since it gives an approximate sense of how large a group is. For instance, the phylum Echinodermata can be assumed to be a major division of life that could contain very different organisms, whereas the genus Schistocerca is probably composed of very similar organisms.
The acronym Didn’t King Phillip Come Over For Good Soup is often suggested as a memorization tool.
In addition to the standard ranks most ranks can be made bigger by adding “super” as a prefix (e.g., a Superoder is bigger than a Order) or smaller by prefixing “sub” (a Subphylum is smaller than a Phylum).
The Linnaean System is Breaking
Modern classification can allow us to see very precisely how species are related. The Linnaean system gives us eight levels of relatedness, with up to twenty four if we use super and sub prefixes on every level. However, in modern classification schemes there can be far more than twenty four levels.
An example will help illustrate this. Mammalia has always been considered to be a Class. The blue whale, Balaenoptera musculus, is a species. In traditional Linnaean classification we can start at Mammalia and work our way to species like this:
However, if we use a modern classification scheme we end up with far more levels between these two points. I am here using the Open Tree of Life web project’s phylogeny.
- An unnamed group containing the Perissodactyla, Cetartiodactyla, and Chiroptera
- An unnamed group containing just the Perissodactyla and Cetartiodactyla
- An unnamed group containing the Cetacea, Hippopotamidae, Ruminantia, and Suina
- An unnamed group containing the Cetacea, Hippopotamidae, and Ruminantia
- An unnamed group containing the Cetacea and Hippopotamidae
- A group containing all mysticetes except the Balaenidae
- Everyone in the prior group except the Neobalaenidae
- The genus Balaenoptera does not exist in this phylogeny. Instead, the blue whale is grouped with Balaenoptera omuraii, B. borealis, B. edeni, and B. brydei
- Balaenoptera musculus
It would be impossible to fit Linnaean levels to all of these groups. So we don’t.
The Cladistics Revolution
Linnaeus grouped animals based on perceived similarity. After Linnaeus a gradual trend emerged to use a more objective method to group animals. Many animals that appear to be similar in general appearance are very different in the details because they have evolved to do the same thing from unrelated ancestors.
The cladistics revolution is a complicated event but the major impacts are described here.
First, in the cladistics revolution a system, called cladistics, arose of attempting to determine the evolutionary history of organisms without having detailed fossil histories. From this arose the idea that species could be grouped based on their evolutionary history. The evolutionary history of a species or group is phylogeny, and it is often displayed as a branching tree. In the cladistics revolution it was decided that taxonomy should reflect phylogeny. This means that a named group should correspond to an evolutionary group.
Most important to this is the concept of monophyly. A group should include all descendants of an ancestor, not just some of them. This means, for instance, that birds, which arose from dinosaurs, are dinosaurs. They are also still birds, because there is some ancestral bird from which all birds arose, but birds are now a subgroup of dinosaurs. Similarly, Linnaeus’ old group for fish disappeared, because the last shared ancestor of all fish is also shared with all other vertebrates.
In the blue whale example above the genus Balaenoptera did not exist because the phylogeny showed that another genus, Megaptera, was also descended from the most recent common ancestor of all Balaenoptera whales.
Second, the word “clade” appeared. Any monophyletic group is a clade. The Kingdom Animalia is a clade. The three species of zebras are a clade. The strange groups in the example in the last section are all clades. When in doubt, say clade.
Clade is similar to the word taxon in that both refer to a group of any size. However, clade refers to monophyletic groups and taxon (plural taxa) refers to named groups (whether or not they are valid groups).
Naming clades can occur in a variety of ways. The PhyloCode is an attempt to codify naming clades in a useful way, similar to what the ICZN is for the Linnean system. Unfortunately, after more than twenty years of work, the PhyloCode is on draft 5 and no definite implementation date is in sight. However, the PhyloCode drafts do outline ways to define clades that are widely used.
Assume the phylogeny below:
This phylogeny shows the relatedness of A, B, C, D, and E. N1 – N4 are extinct ancestral species that are termed “nodes”.
We could define a clade by saying, “All descendants of N1.” Problematically, we rarely actually know what N1 is, merely that is must exist. Instead, we will probably say, “The clade originating from the most recent common ancestor of A and B.” A and B have three named common ancestors in this tree: N1, N4, and Ancestor. However, N1 is the most recent. Similarly, “The clade originating from the most recent common ancestor of D and E,” is all descendants of N3, which are C, D, and E. These definitions are called “node based” because they define a clade by defining a node from which the clade originates.
We could also define our C, D, and E clade by saying, “The least inclusive clade to include both C and E.” Any clade that includes C and E must include D or it won’t be monophyletic, and so the smallest possible clade that includes C and E will be C, D, and E, which is the clade composed of N3 and its descendants.
Another way of defining clades is termed either “branch-based” or “stem-based”, which is confusing since “stem” and “branch” normally mean different things in phylogenies. This method of defining a clade might work like this: the C, D, E clade is the most inclusive clade that includes C but not A. Starting at C we include N2 (and therefore D). We then include N3 (and therefore E). Now we stop, because including N4 would include N1, A, and B, and we explicitly said that A wasn’t in this clade.
Note that these clades are defined in such a way that their membership can change. If I named the most inclusive clade that includes C but not A “Ced” we would currently believe that Ced includes C, D, and E. If new work shows that D is actually most closely related to B suddenly Ced just includes C and E. But that’s fine – we know exactly what is or is not supposed to be in Ced because it has a clear definition. Instead of arguing whether Ced “exists” we can argue about whether species D is in Ced.
We can also use the concept of an apomorphy (a shared derived characteristic) to define a clade. Imagine that A and B are both furry, but C, D, and E are not. We could define clade Abb to be the clade that includes the oldest ancestor of A to have fur that is synapomorphic with the fur A has. (This is slightly tricky, in that if fur has evolved and been lost multiple times in the lineage leading to A we want only the ancestor that evolved the “same” fur that A has today.) However, if it later turned out that fur evolved in N4 and was lost in N3 then we would have to include every single species in this tree in Abb.
Go to Vertebrate Diversity
Tschopp, E., Mateus, O., & Benson, R. B. J. (2015). A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda). PeerJ, 3, e857. https://doi.org/10.7717/peerj.857