Classification, taxonomy and phylogeny of animals

There are at least 5 million different species of living organisms on our planet. From these less than 2 millions have been identified and described and some researcher believe that more than 40 millions species are alive today. These of course does not includes the millions that lived on the earth since life first appeared on our planet 3.5 billion years ago. More that 75% of these living species belong to the Phylum Arthropoda which includes such diverse organisms as lobsters, crabs, shrimps, barnacles, scorpions, spiders, mites and insects. Of course they are many other groups of organisms (think off jellyfishes, mammals, mollusks...) and many more life forms lived in the past geological times. We like to bring order to the chaos around us by classifying things, placing them in to categories. How are these many species of organisms arranged, categorized and classified. The first to attempt a animal classification based on objective structural similarities was the Greek philosopher Aristotle ( 384-322 BC) but most of today principles of taxonomy (Greek taxis : "arrangement, order" and nomos, "law") are borrowed from the work of the swedish botanist Carl von Linn (1707-1778).

The work of Linnaeus

Linn (or Linnaeus in Latin) produced an extensive system of classification (from the Latin classis, "a class", and facere, " to make") of plants and animals. This scheme, published in his great work De Systema Naturae (About the structure of Nature) in 1758, used morphology for arranging species and gave each one a distinctive name. He then grouped similar species into genera (sing. genus) and genera into families then into orders, classes, phyla and finaly into kingdoms. Linnaeus main contribution was to provide order and method in the classification of living organisms by using a hierarchical classification and a binomial naming system.

Classification
Linnaeus' scheme of arranging organisms is a hierarchical system of classification. The major categories, or taxa (sing. taxon) are given one of several standard taxonomic ranks to indicates the levels of similarities between all the members of the group. The system has been considerably expanded since Linnaeus and includes 7 mandatory ranks: in increasing level of similarities kingdom, phylum, class, order, family, genus and species. All species described must belong to at least 7 taxa , one at each of the mandatory level. Taxonomists have the option of subdivizing these 7 ranks into further taxa (superclass, subclass, superorder, suborder, subfamilies, etc.) for any particular group of organisms. Today, more than 30 taxonomic rank have official status and used in particularly large and complex groups such as insects.

Binomial nomenclature
Linnaeus' system for naming species has not changed since the publication of Systema Naturae. Each species has latinized name composed of two distinct words. This system is known as the binomial nomenclature. The first word is capitalized and describes the genus of the species, the second the species itself or species epithet. Both names are written in italic in printed text and underlined in documents written manually or typewritten. The genus is a noun and the species epithet is an adjective which is (or should be) gramatically in agreement with the noun. Any citation of a species must include both names. All ranks above the species are capitalized but only the genus is italicized. All the rule of taxonomy are contained in a document : the International Code of Zoological Nonemclature (ICZN). All names must be unique, universal and stable. Unique Every name has to be unique. If several names have been given the same tazon, priority decides which name with be valid and maintained. Universal Zoologists have adopted by international agreement the use of Latin in biological nomenclature. Stable The ICZN prevent, the frequent, akward or abusive changes of species names to provide stability over time.

Classification and phylogeny

After Darwin publication of The origin of species in 1859, taxonomist began to look for a system rather than a classification for grouping species. While a classification groups objects together based on necessary and sufficient objective conditions, a system groups them according to a process similar to the one that makes take the form that they do. The classification is limited in information to the characteristics that were used to create it whereas systems allow generalizations about the objects beyond the specific characteristics that led to their inclusions in a particular group. According to the theory of evolution, species are formed by descent (reproduction) and modification: as a consequence, the process by which species arise or phylogeny (a process here) is a system of grouping organisms. Because, species arise through reproductive isolation and natural selection, a system for taxonomy must be based on descent, must includes the concept of "has a common ancestor with". Modern taxonomy help us to determine which species are most closely related. It can help us determine for instance whether horseshoe crabs are more related to spiders or to lobsters. The phylogeny (a tree of relationships) of a group of species or other taxa, is the evolutionary tree that related extant and extinct species of that particular group. This phylogeny is build using features (formally called characters) that vary among species. We can find characters useful in taxonomy at the morphological level, molecular level or genetic level. The new systematics relied on the distinction between analogous and homologous characters. Analogous characters Analogous characters perform similar functions but are quite different structuraly. Compare for instance the pectoral fins of fishes with the lateral fins of dolphins or whales. Homologous characters

Homologous characters have quite similar stuctures but perform very different functions. The inner ear bones of mammals are homologous to the fish gills. Analogous characters are evidence of convergent evolution in which different taxa solved a fitness problem with the same or a similar solution. For instance, the long teardrop shape is the shape that offers the least resistance to movement in a fluid. Tunas and dolphins have reached the same evolutionary solution to moving efficiently in the water, they have acquired the same torpedo shape although they belong to very different groups of organisms. On the other hand, homologous characters are evidence of divergent evolution, in which an ancestral characteristic becomes adapted to a new role.

The 3 schools of taxonomy

There are two popular theories of taxonomy based on these evolutionary principles: evolutionary taxonomy and cladism (or phylogenetic systematics) and one based on statistical similarities between groups (phenetics). In these3 systems, any group of organims must belong to one of 3 forms: monophyly, paraphyly and polyphyly:

Monophyly A taxon is said monophyletic if it includes the most recent comon ancestor of the group as well as all of the descendant of that ancestor

Paraphyly A taxon is said paraphyletic if it includes the most recent common ancestor of the group and some but not all of its descendant. Polyphyly Finaly, a taxon is said polyphyletic if it does not include the most recent ancestor of the group.

Both the evolutionary taxonomy and cladistics reject the idea of polyphyletic taxa but the phenetics does not. Cladistics is the most restrictive classification system, it rejects both polyand paraphyletic taxa.

Evolutionary taxonomy
Evolutionists sought to systematise existing Linnean categories, rather that to create new evolutionary groups.The groups that seemed most similar were assumed to be most closely related and similarly, morphologically distant species would share a common ancestors much older than morphologically close species. Ancestral form were deduced either from fossil records or from "living fossils" which do not show significant evolution for several millions of years. This evolutionary system recognises the existence of paraphyletic taxa when the

evolutionary process is sufficiently strong to allow the new taxa to use environmental resources in an entirely new way. Reptiles for instance are considered valid by the evolutionary taxonomist although they do not include mammals and birds who are offspring of an early common ancestor. The traditional view, dating to Linneaus , is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like th eone below above has been constructed but fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.

Cladism
Cladistics (the science) or cladism (the principle) is a type of systematics developed by Willi Hennig, who attempted to develop a more objective method of classifying organisms. Cladism deals exclusively with monophyletic taxa and reject paraphyly and polyphyly as artificials structures with no validity for generalization. Cladisms ignores shared ancestral characters and concentrates on shared characters derived from a common ancestors. In other words, cladisms concentrates on the apparation of new characters state within the group, not on the maintenance of ancestral characteristics. The apparition of new characters in a group can be visualised by a tree like graphic, a cladogram where each new branch defines a group of species sharing common characters.

In this cladogram, new branches defines successively the apparition of vertebrae and jaws (vertebrates), the apparition of four legs and amniotic eggs (Tetrapoda), the apparition of hair and mammary glands (Class Mammalia). Cladists group organisms based on shared derived characters, not the overall similarity of potential group members. In the example above, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT

factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group. We need to modify slightly the above cladogram to include the birds. One characteristics shared by all birds and reptiles and mammals is the existence of nails and claws. If we include this character into the cladogram we have the following diagram which leads to a very different classification:

The value of cladistics lies in its generation of multiple hypotheses (alternate cladograms) that can be evaluated with additional data, always in the context of parsimony (the shortest number of steps or character state changes is most likely correct). An important question....is evolution always parsimonmious? However, the rigor that cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light and to question past classification based on missing fossil records. Recently for instance, the link between some kind of dinosaurs (that includes the well known Tyranosaurus rex) and birds have been strengthen by the discovery in China of several feathered dinausaurs.

Phenetics
Phenetics is a classification based on the statistical similarities between organisms. All characters are given an equal weight and by measuring large number of characters, it was hoped that a stable classification based on overal similarities between organisms would be reached. This kind of taxonomy has received a great interest with the development of computers were later largely abandonned because phenetic classifications were arbitrary and unstable. However, as molecular techniques became popular and more refined, phenetics enjoyed a resurgence. The sequence of amino-acids in any protein, or the sequence of nucleic acids in the DNA provides a large numbers of equally weighted characters suitable for phenetic analysis. A similarity between organims could be calculated on the bases of the changes or non changes in its proteins or DNA structure.