PROLOGUE: A FEW WORDS ABOUT PHYLOGENY & TAXONOMY

It is though that there are over two million organisms on planet Earth and it is very likely that less than half of these organisms have been identified and named. Whatever the number of organisms living on Earth, it represents less than one percent of the organisms that have ever lived on earth. Making sense of the relationships amongst all these organisms is not an easy process.

Classification is the process of grouping things into categories according to their similarities. The process involves categorizing things into general groups and then subcategorizing the general groups into smaller, more specific groups. Biologists use many things to categorize, such as similarities in shape and structure (morphology) and evolutionary history (phylogeny).

The field of biology that determines phylogeny, names organisms and places them into groups is called systematics. While the specific realm of systematics that actually names organisms and places them into their groups is called taxonomy (“the naming of groups”).

One of the first, great taxonomists was the Greek philosopher Aristotle (384 – 322 BC). Aristotle put organisms in groups based on their morphology or shape and called this organization scheme Scala Naturae (“the scale of nature”).

Figure 7.1: Scala Naturae

In the 18th century a Swedish naturalist named Carolus Linnaeus (1707-1778) helped develop the standard system for classifying and naming organisms that is still used today. This system grouped organisms into smaller and smaller groups called taxa (or taxon, singular). In 1735, Linnaeus published his system of classifying organisms as the book Systema Naturae (Systems of Nature). The 10th edition of this text (1758) is considered the starting point for modern zoological nomenclature. However, Linnaeus believed that the shapes of animals were due to God.

The order of taxa used in classifying organisms (from largest to smallest) is shown in the figure below:

Figure 7.2: Taxa used in taxonomy

Linnaeus also was the first to consistently use the binomial name (two names) for organisms. In this system, an organism is named using its genus and then its species name. Under his system, we as humans are known as Homo sapiens. Our taxonomic classification is shown below.

Determining the evolutionary history, or phylogeny, of an organism so that it can be placed into a taxon is not easy. Phylogeny mainly relies upon the morphology of the organism and the use of fossils to see how this morphology has changed over time. Phylogeny involves determining and recording the physical, chemical, embryonic and behavioral characteristics of each species. The recorded information of different species is then compared. If two species are found to have many of these characteristics in

Figure 7.3: Human Taxonomy

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common, they are considered to have a close evolutionary history. On the other hand, if two organisms are found not to have many of these characteristics in common, they are not considered to have a close evolutionary history.

The characteristics of different species that have evolved from the same origin are called homologous characteristics and the degree of similarities amongst homologous characteristics indicates closeness of phylogeny. The field of systematics compares all of the known homologous characteristics of living organisms and the fossil record to determine phylogenetic relationships.

Biologists can take these phylogenetic relationships and create a phylogenetic or evolutionary tree based on homologous characteristics and the evolution of these characteristics. In a phylogenetic tree, you can get a sense of how organisms evolved by looking at where the “branches” of the tree meet. This meeting point represents the common ancestor. More than bone branch can radiate off of this common ancestor. You will see many examples of phylogenetic trees throughout this course

Alternatively, biologists can take these homologous characteristics and create a cladogram. A cladogram is a bifurcating tree that shows relationships among organisms based on homologous characteristics. Technically, a cladogram also does not show evolutionary relationships. In a cladogram, you ask a question about whether an organism possesses a characteristic. If the answer is yes, the organisms goes into one branch of the tree. If the answer is no, it goes in the other branch. The field of biology involved in making cladograms is called cladistics. The cladogram is divided up into groups called clades.

Figure 7.4: A cladogram and the classifying characteristics used to generate it. For example, if the organism does not possess a jaw, it is put into a specific group (i.e. lamprey). The remaining organisms that do possess a jaw go in the other group and are classified further using more defining characteristics.

Class Exercise: Drawing a Cladogram

Draw a cladogram in your lab manual using the information given below for the organisms of this cladogram. The name of the organism is on the left and its characteristics are on the right.

Horse pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae, jaws, tetrapod, amniotic egg, hair

Shark pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae, jaws

Lizard pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae, jaws, tetrapod, amniotic egg, scales

Sea squirt tunicate pharyngeal gill slits, notochord, dorsal nerve cord

Frog pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae, jaws, tetrapod

Lamprey pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae

Pigeon pharyngeal gill slits, notochord, dorsal nerve cord, vertebrae, jaws, tetrapod, amniotic egg, feathers

With the study of DNA, phylogeny and cladistics added a new approach – the study of genetic relationship. You would think that those organisms that look alike and are found in the same taxon would also share an evolutionary, phylogenetic relationship. For the most part, you would be right. However, there has been a recent re-ordering of some organisms in their taxa as we have begun to compare their DNA sequences.

For example in 1969, life on this plant was grouped into 5 kingdoms:

1. Kingdom Monera – single celled organisms that lack a nucleus (includes bacteria, blue-green algae/cyanobacteria and archaebacteria)

2. Kingdom Protista – single celled organisms that possess a nucleus and are eukaryotic

3. Kingdom Fungi – single and multicellular organisms that absorb food through their bodies following decomposition

4. Kingdom Plantae – multicellular organisms that make their own food through photosynthesis

5. Kingdom Animalia – multicellular organisms that ingest their food

In the 1980s, following genetic analysis, a rearrangement happened. We now classify life on this planet into 3 Domains:

6. Domain Bacteria – single-celled organisms lacking a nucleus (includes most of the prokaryotes found in Kingdom Monera)

7. Domain Archaea – prokaryotes that exhibit extreme environments and have DNA sequences distinct enough from bacteria and cyanobacteria to warrant another group

8. Domain Eukarya – eukaryotic cells (including protists, fungi, plants and animals)

While not much happened to the classification of fungus, plants and animals (outside of putting them together in one big domain), a lot of changes happened to the prokaryotes. The major change was the creation of a new Domain known as Archaea. This was done because DNA analysis of archaebacteria showed that these organisms had DNA sequences with enough differences to warrant their removal from Kingdom Monera. In fact, some of the DNA sequences of members of Domain Archaea are closer to eukaryotes than prokaryotes! So Kingdom Monera was split up into two Domains and the remaining kingdoms got grouped into Domain Eukarya.

Each of these domains is made up of Kingdoms. For example, Domain Eukarya can be divided up into the Kingdoms: Protista, Fungi, Plantae and Animalia. Domain Archaea contains 5 kingdoms. Domain Bacteria, however, only has one Kingdom – Eubacteria (meaning “true” bacteria).

The use of the designation Kingdom is not without controversy. There are some taxonomists who think the classification clade of Kingdom should be eliminated and the clade Domain broken up into smaller clades called Phyla. In this class, we will continue to use the designation Kingdom.

An Explanation of Taxonomic Classification

A species is defined as a group of organisms that can interbreed with one

another to produce fertile offspring. An example is the dog (Genus: Canis; Species: familiaris). All dogs can successfully interbreed with one another and are considered the same species. However, when a horse and a donkey interbreed, they produce a sterile mule. So they are considered two distinct species. Some biologists estimate that there are at least 10 million different species of organisms, of which only 1.5 million have been studied!

Species that are phylogenetically related are placed into a larger group called a Genus . The Genus name is always capitalized, whereas the species name is not. You will see that the name of an organism is its Genus and its species name put together with italicized font. Remember that Linnaeus was the one to start to consistently use the Genus and species name to name an organism.

Common dog: Canis familiaris

Common cat: Felis catus

Chicken: Gallus gallus

Bovines: Bos Taurus

Corn: Zea mays

You can think of the Genus as being like your family surname and the species name as being your first name. Using the example of the horse & donkey, there are 9 species that are grouped into the Genus known as Equus. This would be like you and your 8 brothers & sisters. You are all part of the same family but are different individuals (that shouldn’t interbreed!).

Common Horse: Equus caballus

Donkey: Equus asinus

Zebra: Equus burchelli

When referring to the Genus group, but not the species, you can write it like this:

Ursus sp. – a species of bear

Canis sp. – a species of canine

Members of the same Genus share specific traits but not every trait is shared amongst all the members of a Genus. The differing traits allow them to be classified further into distinct species. For example, the common dog belongs to the Genus known as Canis. One of the major characteristics that all members in this genus share is the presence of well-developed canines. Thus the Genus name Canis. Members in this Genus are commonly referred to as canids and include not only the domestic dog, but wolves, coyotes and jackals. All members in this Genus descended from a common ancestor.

The next largest taxon is Family. Family names are assigned by taking the Genus name and modifying it. The Family name will also have an “ae” added to the end of it. Therefore, the family name of the Genus Canis is Canidae. Other examples are:

Cat family: Felidae

Horse family: Equidae

Bear family: Ursidae

Rose family: Rosaceae

Like a Genus, members of a Family share common traits, but fewer than those that the members of a Genus share (and even fewer than those of a species share). This means that members in a Family might look somewhat similar but the members of a Genus will look even more alike. All members in a Family descend from a common ancestor.

You can do the same thing for the next highest level – Order and the next one – Class – all the way up to the Phylum and even the Kingdom. As you progress “up” the taxonomic “ladder” the number of traits shared by the members decrease until you get to Phylum, where members might share only one or two common traits. But the important theme is common ancestor. Members of a Genus share a common ancestor possessing specific homologous traits. Members of a Family share a common ancestor possessing specific homologous traits. Members of an Order share a common ancestor possessing specific homologous traits. Members of a Class share a common ancestor possessing specific homologous traits. Even the members of a Kingdom shared a common ancestor. You might have to look back tens of thousands of years or even hundreds of thousands of years in the evolutionary history to find it – but it will be there.

Don’t think that just because two animals look alike they are closely related and they share a common ancestor. A great example is the flying squirrel and the sugar glider. The sugar glider is a marsupial that is found in Australia, whereas the flying squirrel is a placental animal found in North America. Based strictly on their morphology, you might think they belong in the same Family or even Genus. They do not. These two animals do not share a common ancestor and evolved separately from one another. We call this convergent evolution. You can also think of it as parallel evolution – two organisms evolving along a parallel course but starting from two difference ancestors. If two organisms evolve from the same ancestor, we call this divergent evolution, because the two organisms diverged from the common ancestor.

Figure 7.5: Sugar gliders and flying squirrels

NOTES: Use this space to make any notes regarding this laboratory