Biological Classification, Part One

I’m going to be talking a lot in this blog about different kinds of living things. I may refer to their species name or the family to which they belong or their class and more. So it seems like a good idea to get on the same page as far as what all those classifying terms mean.

Let’s start with the term “species”. Just in the two entries about Yellowstone, I’ve mentioned around sixteen different species. In the most basic sense, a species is a group of organisms that are all considered to be the same thing. Not identical, like twins, but the same type of organism, like all humans are considered. In The Road To Yellowstone, Part One, I compared a mule deer with a white-tailed deer. These are two different species. All the mule deer in the world are considered one species, officially called Odocoileus hemionus.

Official, scientific names use Latin or “Latinized” words so that bias is not given to any currently used language in the world. The purpose of scientific names is so that all people in the world, in any language, with a variety of common names for the same thing, can know that they are all talking about the same species. The person who discovers a species gets the right to assign it a name. Sometimes they pick a name that does, in fact, mean something similar to a common name in their own language. Urocyon cinereoargenteus means “tailed-dog, ashen-silver”, which is pretty close to the common name “gray fox”. Sometimes a species is named for the area in which it was discovered. There are a lot of organisms named “virginiana” and “canadensis”, for instance, which are “Latinized” forms of Virginia and Canada. Some scientists get creative, and/or narcissistic, and throw their own name into the mix. Various plant names have “wrightii” or “greggii” as part of the name. For mule deer, Odocoileus means “hollow tooth” in Latin and hemionus means mule (actually half-mule). So the names do not always make sense at first glance, but there is usually some good reason for the scientific name. In this case, deer in this group do have hollow teeth and the mule deer in particular has large ears like those of a mule.

When two mule deer mate, they have offspring that can grow up to mate with other mule deer and so on. One of the more technical ways of defining a species is that they must be able to have viable offspring. Just because two individual organisms mate and have offspring, that doesn’t necessarily make them the same species. A female horse and a male donkey can produce an offspring but they are not the same species. The offspring they produce is called a mule (not a mule deer!). Because the horse and donkey DNA don’t match up well enough, the mule itself is not able to create sex cells (sperm or eggs). Without sex cells, mules are not viable. They cannot produce more mules by mating with other mules. That means horses and donkeys are not the same species.

The same goes for mule deer and white-tailed deer. If they were to mate, and an offspring was created, it would not be viable, so they are separate species. In nature, it is unlikely that they would mate anyway. Though the two types of deer may look like the same thing to many of us as humans, they may look very different to the deer themselves and would not willingly choose to mate with the other species. Even if looks are not that important to the deer, they may prefer different living conditions, which would keep the two species separate and unable to mate. Whatever the reason, Odocoileus hemionus (Mule Deer) and Odocoileus virginianus (White-Tailed Deer) are different species.

But you may notice something familiar about their official names. Just as both species have the word “deer” in their common names, they each have the word “Odocoileus” in their official/scientific name. That is a clue that they are both similar types of deer, each with hollow teeth, even though they are not the same species. Odocoileus is actually the name of a grouping to which both deer belong, called a genus (plural is genera). There are three species of deer in the world that are similar enough to be in this grouping, just above the level of a species. (The other species lives in eastern Mexico, called the Yucatan Brown Brocket, Odocoileus pandora.) So a genus is a group of separate but similar species.

Before moving on to the next level, there are a few things to point out about the rules or conventions that biologists have agreed to about naming organisms. You may have noticed that I’ve been putting the scientific names in italics. That’s one convention. Another convention is that the scientific name of a species is actually a combination of the genus and the species names. Odocoileus is the genus for all three deer and hemionus is the species name for the mule deer, so the scientific name of the mule deer species is Odocoileus hemionus. You may refer to the genus Odocoileus by itself but never to the species as hemionus by itself. The third thing to point out is that the genus is always capitalized but the species is not. As with all conventions, there’s nothing inherently correct about these, they just help with communication.

Above the level of genus, things get grouped into families. To continue with our deer example, only three species of deer share the genus Odocoileus, but there are many more species of deer in the world. Just within the United States, there are elk (Cervus elaphus), moose (Alces alces) and reindeer/caribou (Rangifer tarandus). These are not only separate species but belong to different genera. However, these three species and the two deer in the genus Odocoileus are similar enough that they are in the same family, called Cervidae. Notice we’re all done with the italics. Everything above the genus level is not italicized.

We’ve talked about three levels of classification so far: species, genus and family. Based on similarities, multiple species may be in the same genus and multiple genera may be in the same family. The pattern continues upward, with each group getting bigger and bigger. But instead of moving up to the level just above family, I’ll go all the way to the top and work my way back down.

If you haven’t taken a biology course since the 1990s or so, you may have been taught that the highest level of organization for living things is the kingdom. There was the animal kingdom, the plant kingdom, the fungus kingdom and two kingdoms made up of mostly single-celled organisms called “Protista” and “Monera”. Organisms in Protista had a nucleus and other organelles, while those in Monera were the bacteria, which did not have a nucleus or organelles. So Monera was the kingdom of prokaryotes and the other four kingdoms contained eukaryotes. We’ll get into more detail about the differences between prokaryotes and eukaryotes in a different post. The point for now is that the five kingdom system has pretty-much been replaced by a system that now has the category “domain” as its highest level.

With advances in genetics and molecular biology, we started seeing that superficial traits, like the existence of a nucleus, didn’t really tell us some important things about the relationship between organisms. It’s the DNA that gives us the most information. After analyzing the DNA from a wide variety of living things, especially once we discovered some of the “extremophiles” in Yellowstone, scientists saw that some of the things that would normally be in the kingdom Monera were actually more closely related to humans than to the bacteria that would be in the same kingdom with them. Because of this, a system putting all living things into one of three domains was created. One domain is a combination of the four previous kingdoms that contained eukaryotic cells and is named Eukaryota. Animals, plants, fungi and the single-celled organisms with nuclei and organelles are in this domain. The single-celled prokaryotes were then split between two domains. The “true” bacteria went into one domain, called simply “Bacteria”, and the rest went into a domain called “Archaea”. In addition to DNA differences, there are significant differences in the cell walls of bacteria and archaea, among other things. So the three domains are Archaea, Bacteria and Eukaryota.

From the domain level down, the classification system and levels are very similar for each domain. One difference is that three of the former kingdoms have been preserved within the domain Eukaryota, while there are no kingdom-level groups in Bacteria or Archaea. Within the domain Eukaryota, there is still an animal kingdom (Animalia), a plant kingdom (Plantae or Viridiplantae, meaning “green plants”) and a fungus kingdom (Fungi). The kingdom Protista was absorbed a little differently into Eukaryota and no longer exists.

Regardless of whether a domain contains kingdoms or not, there is a mnemonic device that used to be used when the five-kingdom system was around that still applies to the levels of classification below the domains. The mnemonic device is this:

King
Phillip
Came
Over
For
Good
Soup

The first letter of each word in the mnemonic device corresponds to the first letter of each level of classification from kingdom down to species. The levels of classification are the following, showing the plural form in parentheses:

Kingdom (Kingdoms)
Phylum (Phyla)
Class (Classes)
Order (Orders)
Family (Families)
Genus (Genera)
Species (Species)

If there is a kingdom, it contains multiple phyla. Phyla usually contain multiple classes, classes contain multiple orders and orders contain multiple families.

Before we do some examples, there’s one other issue to address. It would be nice if every living thing fit neatly into these categories. In the real world of science, that is not the reality. Scientists who study plants have come up with different categories and subcategories of classification than those who study mollusks or insects or birds or bacteria. Even scientists who study the same things don’t always agree as to the best or “right” way to classify things. Since molecular analysis has only been around for a short while in the grand scheme of things, consistency in classifying the wide variety of living things is still a work in progress. But the structure of these categories at least gives us a starting point.

Since the scope of Experiencing Life includes all living things, we need to pick a classification system that has the same scope. That does not mean it is any more correct than other classification systems, but at least it will prevent confusion if an organism can be classified in multiple ways or if there is disagreement as to how it should be classified. The system we will be using is the one put out by the National Center for Biotechnology Information, or NCBI. Right off the bat, it should be noted that NCBI uses the term “superkingdom” instead of “domain”. Knowing that there are flaws with any classification system, we will commit to the NCBI system and deal with the flaws as they come.

Now, let’s do a few examples. We’ll start with a fairly straight-forward example, the type of worm many people use for fishing, the nightcrawler.

The scientific name for nightcrawlers is Lumbricus terrestris. The cells of these worms contain nuclei and organelles which makes them eukaryotes. That puts them in the domain Eukaryota. Worms are animals so they are in the kingdom Animalia. The kingdom Animalia is divided into many phyla and one phylum contains all the segmented worms, called Annelida.

The phylum Annelida is split into two classes: Polychaeta and Clitellata. Nightcrawlers are in the class Clitellata, since they look like “typical” worms without anything protruding away from the main body. Polychaetes have structures called chaetae and parapodia, which stick out from the main body and make them look less like worms. The class Clitellata is split into ten or so orders, and nightcrawlers are in the order Haplotaxida, which consists of worms that live on land, as opposed to freshwater habitats.

The order Haplotaxida is further split into a couple dozen families. The family to which nightcrawlers belong, Lumbricidae, includes the earthworms.

So here is how nightcrawlers are classified:

Domain: Eukaryota (organisms whose cells have a nucleus and organelles)
Kingdom: Animalia (animals)
Phylum: Annelida (segmented worms)
Class: Clitellata (worms without protruding structures)
Order: Haplotaxida (land worms)
Family: Lumbricidae (earthworms)
Genus: Lumbricus
Species: terrestris

Now let’s do the deer example we started. Deer are animals, so they are in the kingdom Animalia, within the domain Eukaryota. In addition to Annelida, another phylum of the kingdom Animalia is the one that contains all the animals with a backbone. This phylum, Chordata, contains everything from fish, reptiles and birds to humans and deer. The phylum Chordata is split into classes, grouping together the fishes with cartilage, like sharks, into one class, bony fish into another class, while amphibians and birds get their own classes. The class to which the deer belong is the one containing all the mammals: Mammalia. The class Mammalia is made up of multiple orders of mammals, such as primates, rodents and carnivores.

The order to which deer belong is still in the process of being clarified in the NCBI system as of 2018. Before DNA caused scientists to reevaluate old assumptions based on physical traits, deer were in an order called Artiodactyla, which was basically all of the split-hoofed animals. The animals that were in the order Artiodactyla are still considered closely-related, so for the purposes of our example, we’ll pretend the order still exists. The order Artiodactyla contains a variety of families, including the families of hippos, pigs, camels, giraffes, cows and deer. The deer family, as mentioned above, is Cervidae.

So here is the summary of how the mule deer is classified:

Domain: Eukaryota (organisms whose cells have a nucleus and organelles)
Kingdom: Animalia (animals)
Phylum: Chordata (animals with backbones)
Class: Mammalia (mammals – animals with mammary glands)
Order: Artiodactyla (split-hoofed mammals, not technically an order as of 2018)
Family: Cervidae (deer)
Genus: Odocoileus (hollow-toothed deer)
Species: hemionus (mule deer)

Let’s do one more example, using a plant this time. Cedar trees and junipers, in the genus Juniperus, can be found all over the U.S. The Red Cedar’s scientific name is Juniperus virginiana and the Common Juniper’s scientific name is Juniperus communis (see how the scientific names refer to a location in the first case and the common name in the second case?). These are just two of many species in the genus Juniperus. Cedars and junipers are similar to other trees like Cypresses, redwoods and sequoias but those types of trees are different enough to have their own genera. However, all of these types of trees are in the same family, called Cupressaceae. The family Cupressaceae actually contains a couple dozen different genera.

There are two other families of plants that are similar enough to Cupressaceae that they are grouped into the same order: Cupressales. The family of yews, Taxaceae, and the Umbrella Pine family, Sciadopityaceae, join Cupressaceae in this order.

Above the level of order, there should be a class to which these plants belong. In the NCBI system, the closest thing to a class for the plants that have cones instead of flowers is Acrogymnospermae, which is similar to the group that used to be called “gymnosperms”. This group contains not just typical conifers, like the pines and cedars we’ve already mentioned, but also plants called cycads, gnetophytes and an ancient type of tree called Ginkgo.

In the NCBI system, this class-level group called Acrogymnospermae joins nearly all other plants in the phylum Streptophyta. This phylum includes everything we’ve talked about so far, which are the plants that reproduce with cones, and adds all of the flowering plants, the ferns and even the mosses. Since this phylum is made up of everything except the simplest of plants, the phylum is sometimes referred to as the “higher plants”. The only plants that are not in this phylum are the mostly single-celled organisms often referred to as green algae. Even the green algae are similar enough to cedars and flowering plants to be included in the same kingdom of plants, called Viridiplantae. The entire kingdom is a subset of the domain Eukaryota.

As a side note, here’s another example of how classification systems can get confusing. The scientists who study plants, called botanists, have long used a different word for the level of phylum. Instead of phylum, they use the word “division” to refer to the exact same concept. Here at Experiencing Life, we will use the term “phylum” uniformly.

So the classification for a red cedar is the following:

Domain: Eukaryota (organisms whose cells have a nucleus and organelles)
Kingdom: Viridiplantae (green plants)
Phylum: Streptophyta (“higher” plants)
Class: Acrogymnospermae (cone-bearing plants)
Order: Cupressales
Family: Cupressaceae
Genus: Juniperus (cedars and junipers)
Species: virginiana (red cedar)

Those examples should at least get us on the same page as far as the basic terms of classification.

One last thing to mention is that classification is a dynamic process. The way something is classified may change slightly when new information comes to light. That fact should not distract from the goals of Experiencing Life. If you experience an organism that you think is part of a group unique enough to have it’s own phylum and then you later learn that the group is more likely to comprise a class within another existing phylum, that should not take anything away from the experience. Whether Peanut Worms are a subset of the phylum Annelida or they deserve their own phylum, it is still exciting to see this relatively rare type of worm.

The point of Experiencing Life is to appreciate the wide variety of living things, regardless of the way they are classified. So we’ll use the NCBI system as a guiding structure and as a way to share common terms. Beyond that, experience what you want to experience!

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