Organisms Can Be Classified
Clickable Hierarchy of Classification
Biological Classification
Organism Names
Number of Organisms
Number of Kingdoms
Cladistic Phylogeny

We have learned that Biology is hierarchical having at least these levels:

You might notice above that the level of organism is highlighted, which is perfectly appropriate for this course! So, while biology has all of those levels of organization, we focus in this course mostly upon the individual organism. The big idea for today is to understand that when we look at the organisms, we also find that this single layer itself has many layers in another dimension. Rather than levels of organization, the organisms show incredible diversity that we distinguish in a process often called classification.

There are many ways that the organisms might be classified. Humans have traditionally grouped organisms into some major groupings and then subgroupings within each group. Humans love hierarchy, and so we naturally understand how to organize a complex mixture of organisms into groupings. This classification process could have placed the organisms into categories of usefulness...for example: those that provide food, those that provide fuel, those that provide clothing, those that perform work, those that provide pleasure, etc. But of course plants and mammals can supply food, and they can provide clothing. So this kind of classification would be defective in that it would put dissimilar organisms into the same groups...and similar organisms into different groups. So classification by usefulness would be unnatural. Obviously something less practical but more natural was needed to be biologically significant.

Biological Classificationé.jpg

Carolus Linnaeus (aka Carl von Linné) developed a hierarchical classification scheme that continues to be biologically useful to this day. This method compartmentalizes all of the organisms on the planet into categories based upon their characteristic features. So their form (morphology), internal organization (anatomy), physiology (function), reproduction (sexual features and functions) are used to group similar organisms into a few major groups called kingdoms. Sorry ladies, but this was designed in a male-dominated culture, so there are no queendoms. These major groups include one for plants (named Plantae) and one for animals (named Animalia).

Kingdoms are obviously quite large and include a lot of organisms. Obviously some more classification was needed. So each kingdom was divided into some subdivisions called phyla. Each phylum was divided into classes, each class into orders, each order into families, each family into genera, each genus into species. So biological classification has layers like an onion is hierarchical. The table below shows the classification names at each layer (taxon) for six specific organisms.

Gram +
SpeciesE. coliH. salinarumF. distichusR. multifloraA. bisporusH. sapiens
CommonDH5αHalophytic archaeanRockweedWild RoseMushroomHuman

The rows in this table represent the layers of classification among organisms. The first column provides the name for each layer of taxonomy. The remaining columns give the taxa for each of six organisms.

You might notice that in some cells of this table, there are multiple entries. In taxonomy there may be multiple names in use for the same taxon. For example, the phylum of the flowering plants is known as Anthophyta by some and Magnoliophyta by others. These two names for the same plants are called synonyms.

You might notice that some taxa in a particular row of the table share similar endings (e.g. -ales for the family taxa). Again, while we might portray taxonomy as "universal" there are some taxa in use that do not conform universally.

Names for Organisms

The lowest row in this table gives the common name of the organism in the column. Common names are, of course, not unique or universally understood and so they have little place in science. So while they are included here for illustration, in biology we tend to use only the scientific name for each species. The scientific name for a species is the combination of the Genus name and the Species epithet; it is thus a double name (a scientific binomial). You might notice that your human binomial is Homo sapiens, sometimes abbreviated H. sapiens. As a matter of common literacy for college students, you should learn your binomial and how to spell it! Remember, you needed to know your personal common name and how to spell it for first grade? Well, now we expect you to learn one more! Notice how Homo sapiens ends in the letter s; that letter must be present whether you are talking about one individual Homo sapiens or many Homo sapiens. You are expected to know and spell this correctly from now on!

The other observation you might make of scientific names is that they are Latin names often with Greek roots as well. Since these are Latin rather than English, it is proper to show them in italics in print but should be underlined in manuscript. The roots for our human binomial have meaning...Homo means self; it identifies us as the organism responsible for the taxonomy! The epithet sapiens means that we are capable of reasoning. Apparently we consider this to make us unique among the organisms...but that is somewhat controversial as you might guess.

Scientific names are not made by combining a descriptive name in English with a -us suffix as is commonly observed on television cartoons. A coyote is not called Wolfus stupidus or Caninus acmeensis. The coyote's correct binomial is Canis latrans (dog barking) which makes it a member of the same genus (type of organism) as the wolf (Canis lupus--dog wolf) and the dog (Canis familiaris--dog household). In fact these three species can interbreed quite easily.

A. Coyote
B. Wolf
C. German Shepherd Dog
D. Coydog
E. Wolfdog

Number of Organisms

A natural next question might be to quantify how big the classification task really is. How many organisms are there on Earth? This question is difficult to answer because, in spite of the many years of human observations and naming many, many organisms, we know there are many species yet undiscovered and undescribed on our planet! There is more work for your generation of scientists to do!

If we consider the commonly-described six kingdom taxonomy, reasonable estimates might be:

These round numbers will surely be wrong if we ever get to know all of the species on our planet. But it is worthy to notice that animal species are most-numerous. However, I would point out that arthropods (jointed leg organisms, mostly insects) represent over a million of those species! And, among the very numerous plant species, the vast majority are flowering plants.

Another interesting question is how a biologist knows whether two organisms are different enough to be different species. In fact, this is not a trivial question. In ancient days of science, a species concept was advanced that if two organisms could successfully mate, then they were the same species. Of course for some species, sexual reproduction is unknown, so this could not be used for them. In other cases, offspring are produced but are defective. For example, if a mare horse is mated to a jack donkey they produce a mule. Because mules are usually sterile, donkeys and horses were considered to be different species. It is impractical if not impossible to do the controlled matings to carry out this kind of "test" for the millions of species listed above. Plus it turns out that if we get away from mammals, matings between quite different species can sometimes produce not only viable offspring, but fertile ones too! If you ask a botanist to identify an oak tree on campus, there might not be a fast and direct answer. The red and black oaks mate easily but the offspring double their chromosomes spontaneously to become fertile new species! These new species can mate true to their hybrid type...but can also produce yet other "hybrid" species by mating back with the parental species. So what we see in the forest is, in fact, a hybrid swarm of strange combinations of oak species.

You can imagine the difficulty for scientists of coming up with unique names for each of the millions of species! Common names are much easier to coin, fewer are needed, they can vary from language to language, from location to location, and they are not necessarily unique. One common name for an organism is "Black-eyed Susan" but there are over 200 different species that have this common name in one place or another. So common names just do not provide the level of specificity needed for science! Official Latin binomials are unique to each species and the legitimate name is universal so that all scientists can be sure of the species used in a particular study. Having said that, however, it is also true that as scientists study the biological literature they find that earlier binomials had been coined for a particular species. Because the earliest name has priority over later coined binomials, the binomial can be changed...and this leads to some synonyms for a species. While all scientists should change to the earliest and official binomial, sometimes the newer binomial has become so ingrained in the literature that it continues to be used.

As an example of this phenomenon, I'll cite my own experience. I was working with the Morning Glory vine. When it came time to publish my work, I noticed that the plant physiologists who study this plant use a newer (deprecated) binomial, Pharbitis nil, rather than its "official" name, Ipomoea nil. So which should I use in my paper? I decided to use the correct name in the title and most of the article, but did list the "common use" binomial as a synonym at the beginning of the manuscript.

Taxonomy is a dynamic study, however! The groupings above the level of Genus are often revised as new information makes older groupings less than perfectly natural. In recent years, information from DNA or protein sequences have been used as characteristics to regroup organisms into different alliances at higher levels of taxonomy. And, as we shall see, the kingdom-level taxa have changed dramatically over the years...and will continue to change!

Number of Kingdoms

In the early to mid-1900s biologists considered all the organisms to fall into two kingdoms...Plantae and Animalia. This first level of classification seemed easy. Organisms that could locomote (move from place to place) were animals, and those that could not move were plants. Of course this simple division was too superficial and put many sessile animals into the plant kingdom. And among the plant kingdom there were many organisms that just do not share many other attributes with plants. Obviously the plant kingdom was artificial and had to be divided into more natural groupings. So additional kingdoms were needed.

One of the earliest kingdoms to be divided out were those organisms that lacked a nucleus or organelles in their cells...the prokaryotic organisms. Kingdom Monera was the result, and it contained all the bacteria and related organisms of the prokaryotic type. So now there were three kingdoms.

Among kingdom Plantae another large group with commonly-shared characteristics was distinguished. They lacked cellulose cell walls, using chitin instead. Their life history was more like animals than like flowering plants. So a fourth kingdom was separated out called Kingdom Fungi. This includes the molds, mildews, and mushrooms. They really are not plants and are, in fact, closer to animals in most of their characteristics.

Another group of organisms were really difficult to assign to any of these kingdoms. Some had characteristics leaning toward prokaryotic assignment to Monera, others had plant-like feature leaning toward Plantae, others were sort-of fungal leaning toward Fungi, and yet others were animal-like leaning toward Animalia. Making matters worse, there were organisms that had features somewhere in-between kingdoms. All of these difficult-to-classify organisms did have some features in common...they were fundamentally unicellular and aquatic. So an artificial (mixed descent) kingdom was created, Kingdom Protista, to hold them. Obviously further study of Protista has resulted in some of these species being moved to one of the other four kingdoms. Further study of this group will create newer kingdoms as well.

A bit later, further study among prokaryotic organisms discovered that Kingdom Monera was also an artificial kingdom. Some of these species have introns in their DNA, have different cell wall material, and many other features in common, but separate from the common bacteria. So Kingdom Monera was deprecated and split into two new kingdoms: Bacteria for the true bacteria and Archaea for the rest. If you have followed this discourse mathematically, we are up to six kingdoms. But we are not done!

Kingdom Protista is admittedly artificial and needs a lot more study by your generation of scientists to figure out the natural relationships. Already, we have proposals to split out two more kingdoms from Protista. These two groups have bodies that are multicellular (though they behave mostly as independent single cells) in a unicellular kingdom. But they also differ in their plastid ultrastructure and biochemistry. One group might be called Kingdom Stramenopiles and will include the brown algae, chrysophytes, and diatoms. The red algae are also a unique group deserving a Kingdom perhaps called Rhodophyta. So we will soon be teaching about eight kingdoms... but there are others in the works. It has been projected that the ultimate resolution of Protista will end up in twelve or more kingdoms in total.

These changes in the number of kingdoms is shown in the table below. Each row of this table represent a group of organisms. The color of the cell represents the kingdom assignment. The columns show the changes in those kingdom assignments over time, so time progresses left-to-right across this table.

Number of Kingdoms
Green AlgaeGreen AlgaeGreen AlgaeGreen AlgaeGreen Algae
Brown AlgaeBrown AlgaeBrown AlgaeBrown AlgaeBrown Algae
Red algaeRed algaeRed algaeRed algaeRed algae
Slime MoldsSlime MoldsSlime MoldsSlime MoldsSlime Molds
True FungiTrue FungiTrue FungiTrue FungiTrue Fungi

Taxonomists who tend to recognize more rather than fewer divisions are called "splitters" while those who tend to put groups together into fewer divisions are called "lumpers." It would seem that new information is supporting splitters more than the lumpers these days. But most biology textbooks certainly are written by lumpers. Authors seem to talk about six kingdoms in the taxonomy chapter, but then the book table of contents is clearly divided into two major units...plants and if there were really only two kingdoms and as if the year is 1955. This is why I am writing these pages for you here! There is no biology book in print now that takes the approaches we take here.


Why are the number of kingdoms or other levels of taxonomy so controversial? Why aren't the species groupings absolutely clear? Part of the answer to these questions lies in the simple fact that biology has so many species and that we know relatively very little about most of them. We need an army of biologists to figure out this mess of millions of species on our planet. So many of us are tied up studying just a few species, that most are almost completely unstudied. There is a lot of room for you in this field!

Another important basis for the lack of consensus and lack of clarity is that the diversity of organisms is the result of natural evolutionary processes that are not neatly or easily packaged into the boxes or onion layers of taxonomy. Because of this origin for the diversity, a new thrust in taxonomy has developed since the 1960s. This new way of thinking about taxonomic relationships has focused upon the evolutionary pathways by which species evolved and by which they are naturally related to each other. One could think of this as the study of phylogeny.

In evolution, species diverge to form a branching tree-like organization as time progresses, and so this new taxonomy is about branching patterns in evolution through time. It is called cladistic phylogeny or simply cladistics. Rather than thinking about kingdoms, phyla, classes, orders, families, genera, and species as nested containers for organisms, we think of how they are related to each other by virtue of the characteristics they share, and how they branched about by virtue of the characteristics they do not share.

Below is a dendrogram (a tree-like phylogeny diagram) of a range of organisms covering the breadth of biology. It represents a new way of thinking about classification and taxonomy that most closely ties to evolution.

Across the top of this dendrogram, you can see the names of several kinds of organisms that are found on planet Earth alive right now. Beneath them are branching lines in red that show the pathways of evolution that appear to have been followed to arrive at this group of extant organisms. Thus the vertical dimension of this diagram is Time with the present time at the top and ancient times beneath. You will notice that this "tree of life" goes to a single trunk at the bottom. This of course means that biology shows us that the living organisms on this planet are ALL related through common ancestry going back to the original living cell on our planet.

You might observe that the prokaryotic organisms branch off very low on the tree of life and have evolved separately from the eukaryotic organisms. The fossil record and other geological evidence on our planet is in total agreement with a long period of time with only prokaryotic organisms on our planet. Thus Kingdom Bacteria and Archaea are the original Kingdom(s).

Later, eukaryotic organisms evolved as a new branch on the tree of life...a third kingdom evolved which we might today call a domain. This group diverged into two major lineages, one more plant-like, and the other more animal-like. Further branching shows how the other kingdoms connect to each other.

In dendrograms such as this one, you will notice how several groups cluster into a coherent branch with twigs. The green algae, bryophytes, and tracheophytes are clearly a closely related group. Today we recognize them as Kingdom Plantae... but for this diagram they are known, including their extinct shared ancestors as a clade (a branch with all of its twigs). In a similar way, The chrysophytes and brown algae and their common ancestor (where the twigs join) constitute a clade and we would describe them as Kingdom Stramenopiles.

The bacteria and the archaea and their common ancestors on this dendrogram do not constitute a clade because they are not a branch with all of its twigs...they are a side branch to a clade, so they are what we call a grade.

But the entire tree of life here is a clade isn't it? It shows a common ancestor and all the extant organisms are descendants of that one ancestor. So the tree of life is a clade...and is made of clades and grades.

The red algae (Kingdom Rhodophyta) is a grade to a clade that includes Kingdom Stramenopiles (chrysophytes and brown algae) and much of Kingdom Protista (archezoans, euglenoids, and protozoans).

But Kingdom Protista as currently constituted is polyphyletic (an artificial group of unrelated organisms). Notice how the clade of archezoans, euglenoids, and protozoans and their common ancestor are on a different part of the tree from the clade of slime molds and myxozoans which are considered as part of Protista.

In this way, if the branching patterns in our dendrogram are correct, then the kingdoms Fungi, Plantae, Stramenopiles, Rhodophyta, Archaea, and Bacteria are natural. Kingdom Protista needs further division, and Animalia may need some reorganization too as a result.


Classification of Organisms




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