Introduction

There is, of course, some controversy over the definitions of each taxon (level in the taxonomic tree), and there are many different models attempting to describe the relationship of all living organisms. This article will touch on a few of the more accepted models, starting with the Traditional, or Linnaean System, some variations of this system, followed by Cladistics. 

Traditional, or Linnaean System of Taxonomy

When discussing an organism, scientists often refer to the organism by its binomial, or scientific name. The binomial (bi=2, nomial=name) is a two part name given to every classified organism. The first name is the genus (plural = genera), and is always capitalized, as are all preceding taxa. The second word is the species name, which is always lower case. In literature, is is common practice to italicize both the genus and species when referring to both, or either. For example, the binomial for the red-eyed treefrog is written Agalychnis callidryas, where Agalychnis is the genus, and callidryas the species. Some species have subspecies, the name of which is written after the species name, in lowercase, and also italicized, in a trinomial fashion. The trinomial for the Sierra newt, for instance, is written Taricha torosa sierrae. 

The following describes the main taxa in the traditional system, and some qualifications:

KINGDOM:
In the Kingdom, organisms are distinguished according to cellular characteristics and methods of obtaining nutrition. For example, the Kingdom Monera consists of prokaryotic single-celled organisms that absorb nutrition, while the Kingdom Animalia consists of eukaryotic multi-celled organisms that ingest nutrition. There are five defined Kingdoms of living things: Monera, Protista, Fungi, Plantae, and Animalia. However, Monera and Protista are of particular ambiguity, which will be addressed later.

PHYLUM:
Kingdoms are further divided into Phyla (single, Phylum). Organisms are placed into Phyla according to basic, physical similarities. The Phylum Chordata, which includes humans and amphibians, is divided further into three subphyla: Vertebrata (animals with spinal chords), Urochordata (invertebrates), and Cepalochordata (invertebrates).

CLASS:
Phylums are categorized into Classes. Members of Classes are grouped according to their skeletal system, environmental adaptations, and their reproductive systems. The seven Classes of Phylum Chordata, Subphylum Vertebrata are: Agantha, Chondrichthyes, Osteichthyes, Amphibia, Reptilia, Aves, and Mammalia. 

About Mammalia:
The Class Mammalia is further divided into two Subclasses, Prototheria and Theria. Prototheria includes mammals that lay eggs in the fashion of non-mammalian vertebrates. Examples are Ornithorhynchus anantinus (Platypus), and Tachyglossus aculeatus (Spiny Anteater). The Subclass Theria, which includes all other living mammals, is further divided into three Infraclasses: Eutheria (placentals), Metatheria (marsupials), and Pantotheria (extinct Therian mammals).

ORDER:
Classes are divided into Orders, for which organisms are categorized according to closer morphological similarities. The Class Amphibia includes three Amphibian Orders: Anura (frogs and toads), Caudata (newts and salamanders), and Gymnophiona (caecilians). All frogs and toads share similar traits, as do all salamanders, and all caecilians. 

FAMILY:
Orders are divided into Families, for which organisms are categorized according to more detailed morphological traits. The Orders Anura, Caudata, and Gymnophiona contain 29, 10, and 5 Families, respectively. There is often shuffling of families within the orders as new information is discovered about the members.

GENUS (plural, Genera):
Families are divided into Genera (single, genus), for which organisms are categorized according to even closer similarities. The first word in a species scientific name (Latin name) is the organism's genus, the second is the Species, and if a third word is included, it is the Subspecies. Each Amphibian Family contains one or more Genera. For example, the Eastern Newt, Notophthalmus viridescens is of the Genus Notophthalmus.

SPECIES:
Finally, the last category is the species. The species is the fundamental category in the Linnaean system, but can be followed by a subspecies. Subspecies are only slightly different than their species, and are capable of interbreeding. The second word in an organism's scientific name (Latin name) is the species, and the third is the subspecies (where applicable). For example, the Peninsula Eastern Newt, Notophthalmus viridescens piaropicola, is a subspecies of the Eastern Newt, Notophthalmus viridescens. The subspecies described first is referred to as the nominal form, and has the same subspecies name as the species name. In our Notophthalmus viridescens example, the nominal form would be Notophthalmus viridescens viridescens. Species and subspecies are sometimes further distinguished by classification into Races, according to geographic locations, and/or physical and behavioral differences. Races and subspecies are also sometimes regarded as synonyms. 

The further nested a taxa, for example the Genus level, the closer related the organisms. New methods of analyzing DNA has created doubt among the current classification of many species, and some professionals would say the traditional system is now obsolete. Such proponents would opt for a strictly cladistic approach to categorizing species. Cladistics is based solely on ancestral lineages, and uses the evolutionary history of organisms, attained mainly through molecular analyses, to classify animals (more on Cladistisc below). 

Three-Domain System of Taxonomy

In the three-domain system, all Eukaryotes are included in the domain Eukarya, and the remaining two domains, Bacteria and Archaea, include the Prokaryotes. Formally, this system also includes another domain called Urkaryotes, comprised of eukaryotes prior to their establishment of endosymbiosis with eubacteria (i.e. before the development of mitochondria and chloroplasts).

The domain Bacteria includes all of the "modern" Bacteria, sometimes called Eubacteria. This domain includes all of the commonly known bacteria, including those that cause disease and infections in animals. Others are either non-harmful, or beneficial to their hosts or the environment. 

The domain Archaea is comprised of the ancient bacteria, or Acrhaea. Archaea are not harmful to animals, and are characterized as extremophiles, a reflection of their affinity for the harshest of environments. There are three basic types of Archaea, the methanogens, halophiles, and thermophiles. Methanogens are so called because of their unique way of obtaining energy by using CO2 to oxidize H2, which produces Methane (CH4). Methanogens are strict anaerobes, and die immediately upon exposure to Oxygen. They are found in swamps and marshes, where they expel large amounts of Methane, or swamp gas. Halophiles inhabit extremely salty environments, sometimes in waters more than 30% saline such as the Dead Sea and the Great Salt Lake. Halophiles create a purple-red, sometimes yellow, scum due to the presence of bacteriorhodopsin, a color pigment similar to that found in human retinasa. Thermophiles inhabit extermely hot bodies of water, including sulfter springs and deep sea black smokers. These prokaryotes are found in the temperature range of 60°C-105°C, and are known for their ability to oxidize Sulfer. The extreme conditions preferred by Archaea are reflections of the extreme environment the Earth once was, so many millions of years ago, when Archaea were abundant.

In this system, the domain Eukarya is divided further into varying numbers of "Kingdoms". Some have kept the traditional Kingdoms from the Five-Kingdom model, with the exception of all Prokaryotes, while others have divided the Eukarya into other, varying groups. 

Cladistics, or Phylogenetic Taxonomy

If a shared similarity, such as webbed feet, was derived from a common ancestor, it is called a Homology. Homologies are usually applied and tested against a group of animals thought to be closely related, such as snakes, lizards, and crocodiles. Theoretically, if one wanted to define a more inclusive group, homologies could be documented all the way back to the common ancestor of all life. However this is impractical, probably impossible, and doesn't tell us much about the evolution of a particular species. In most instances, one would attempt to show how closely related certain organisms are based on their divergence from the most recent ancestor. 

Homologies that are derived from the most recent ancestor of a particular group of organisms are called Shared Derived Characters. Shared derived characters are unique to the particular group in question, and can distinguish it from a more inclusive group that may include more distant ancestors. Other characteristics shared with more distant common ancestors, and that may be present in other groups, are called Shared Primitive Characters. Take for example the presence of hair and backbones in the mammalian group. All mammals have both characters, but only the hair characteristic distinguishes mammals from all other vertebrates. This is a shared derived character. Other groups besides mammals possess backbones, and so the backbone is a shared primitive character of mammals. On a more inclusive scale, the presence of a backbone is a shared derived character when applied to the entire vertebrate group, because it is unique to that group, and a result of the most recent vertebrate ancestor. The status of a particular characteristic is dependent on how inclusive the group in question is.

Cladistics is a method of classification that attempts to organize groups, or individual species based on their common ancestors. The basis for Cladistics is the divergence from an ancestral line, whereas with the Linnaean System, the focus is on physical and assumed similarities. In Cladistics, similar organisms are categorized into clades. There are three types of clades, monophyletic, paraphyletic, and polyphyletic. A legitimate, and complete clade is one that includes a common ancestor and all of it's descendents, and is called a monophyletic clade. A paraphyletic clade is one that includes a common ancestor and only some of the descendents, and a polyphyletic clade is one that includes the descendents, but not the common ancestor. The cladogram in Fig. 12.1 shows a simple phylogeny involving several different animals, and their branch-point separation from a common ancestor. In the clade, the main line represents the common ancestor linking all of the animals together. Each branch separation from the main line represents a separation from the common ancestor, and is thus the most recent common ancestor to each animal. During the evolution of the common ancestor to all of the animals portrayed in the cladogram, species branched out as a result of the derivation of unique characteristics. For instance, because the turtle is between the salamander and the wolf, it can be shown that the turtle separated from the common ancestor after the salamander, but before the wolf. This is not to say that turtles are more closely related to wolves, only that turtles shared a common ancestor with wolves more recently than salamanders. The cladogram also does not imply that all salamanders evolved before all turtles, but only that the salamander-wolf common ancestor preceded that of the turtle-leopard clade. 

Listed also in Fig. 12.1 are examples of some of the common traits derived after the split from the common ancestor, for which each preceding animal does not possess. Each animal placed after the listed characteristic possesses that particular trait, as well as all of the preceding listed characteristics. For example, the wolf possesses hair, amniotic eggs (at one point), four-legged locomotion, a jaw bone, and a vertebral column, whereas the turtle, preceding the hair characteristic, possesses all of the traits except hair. Further down the ancestral line, we see that the lancelet possesses none of the traits, and precedes all animals with a vertebral column. Similarly, we see that the lamprey precedes all animals with jaw bones, etc., up to the wolf that possesses all listed traits. All of the similar traits are homologies because they were derived from a common ancestor. This example uses Outgroup Comparison to construct the cladogram. The lancelet is considered the outgroup, because it precedes the group of organisms with vertebral columns. The other four organisms are considered the ingroup, and are essentially being compared to the outgroup in terms of evolution.

Not all similar characteristics are derived from a common ancestor. The wings of a bat and those of a bird, for example, are similar characteristics in that they are both wings, and serve the purpose of flight, but are not homologous because they did not evolve from a common ancestor. Such similarities are called Analogies, and occur when two species develop similar traits, but that are not due to emergence from a common ancestor (convergent evolution). Analogies are usually adaptations to similar environments, or ecological niches. In terms of ancestral lineage, analogies are only skin deep, and do not reflect concurrent emergence from the common ancestor. Fig. 12.2 (a) and Fig 12.2 (b) below show two different clades relating the appearance of a four-chambered heart in a lizard (reptilia), a bird (aves), and a fox (mammal). Fig. 12.2 (a) shows an bird-fox clade, for which the four-chambered heart is a homology of the two animals. However, molecular data supports the hypothesis that the four-chambered hearts of birds and mammals are actually analogous, and the four-chambered heart is thought to have evolved separately in both organisms. Fig. 12.2 (b) shows the current hypothesis, with a lizard-bird clade, excluding mammals, but showing the separate evolution of the four-chambered heart in both birds and mammals. This example shows that morphological characteristics alone are often times not accurate means of classification, as is the basis of the Traditional System of Taxonomy.

So, how can one tell the difference between a homology and an analogy? This is the job of the systemetist, and there are several ways, used in conjunction, to try to determine when and why certain traits were developed in species. The fossil record, although incomplete, provides much insight to the behavior and evolution of many species. Occasionally, soft tissues are preserved in fossils, in addition to the hard materials, which provides even more information about a particular species' evolution. From a fairly preserved fossil, much about the animal can be determined, such as size, weight, gender, diet, gait, etc. The fossil record is often still consulted with new systematic hypotheses, however, new advances in molecular analysis allow scientists to more accurately determine when a particular characteristic was developed within a species. This is most commonly done by comparing sequences of nucleotides in DNA and RNA, which program corresponding sequences of amino acids in proteins. Because nucleotide sequences are inherited, the degree of similarity of sequences between two species indicates how recent their split from the common ancestor. Each of the nucleotide positions in a segment of DNA represents an inherited characteristic, displayed in the form of one of the four DNA bases (Adenine, Guanine, Thymine, and Cytosine). In such analyses, homologous regions in the sequences of two species' DNA that are 10,000 nucleotides long provide 10,000 points of comparison. Such comparisons can prove too tedious to do by hand, so computers have been incorporated to automate much of the work. 

The rates of change in DNA sequencing vary for different parts of the genome, and the coding is rather slow for ribosomal rRNA. Nucleotide sequence comparison of rRNA is especially useful in determining relationships between taxa that evolved several hundred million years ago. In contrast, mitochondria (mtDNA) evolves rather quickly, and is useful in determining relationships between very similar taxa. Recently, this has led to the re-classification of many former species into separate species.

Schuh, R.T. Biological Systematics: Principles and applications. Cornell University Press, 2000.