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Taxonomy and Phylogeny

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Taxonomy is the theoretical study of classification and the principles, procedures and rules thereof. Essentially, taxonomy deals with the ways in which we group living things together. Phylogeny refers to evolutionary history.

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Taxonomy

Taxonomy has a long history, with Aristotle giving the first detailed classification of living things. His classification of animals was:

However, he had made no effort to classify plants or fungi. Modern approaches to taxonomy, while obviously more diverse than in Aristotle's time, but can be lumped into three major schools: phenetic, phylogenetic (cladistic), and evolutionary.

Phenetic Taxonomy

Phenetics is an approach to grouping organisms based on total (or "raw") similarity. Although its history dates back centuries to the French botanist Michel Adanson, phenetics underwent something of a renaissance in the 60's, 70's and early 80's in response to a growing dissatisfaction with what its practitioners viewed as the arbitrary and nonquantitative approaches that rose to prominence in the 1950's. Particularly troubling was the evolutionary taxonomy of Ernst Mayr, George Gaylord Simpson and others (described more fully below) that appeared to be more "art" than science.

On this basis, rigorous computationally-driven clustering methods were developed to combat these perceived problems. Information about organisms would be gathered, fed into computers, and out would come hierarchical arrangements of organisms based on overall similarity, typically arranged in a "tree" of sorts called a phenogram.

It is important to draw a distinction between phenetics as an approach to taxonomy, and phenetics as a tool for deciphering the evolutionary relationships of organisms. Although phenetic clustering can and has been used to generate phylogenetic trees, to the phenetic taxonomist, any convergence of his phenogram on a phylogentic tree is purely coincidental. Even if the groups he were to arrive at phenetically were nothing like the groups we'd discover if we had a chance to look at the true tree of life, it wouldn't matter; there are reasons, they think, for representing living things this way independent of evolution.

Phylogenetic (Cladistic) Taxonomy

Main article: Cladistics

Since the dawn of taxonomic science, its practitioners had arranged groups via the emphasis of certain characters. The group we know as birds were delimited because they all had feathers, and when Linnaeus was writing, were toothless. Invertebrates lacked a notochord, vertebrates possessed one. And while groups appeared to be nested within in each other, this was seen as just another part of God's special creation.

With Charles Darwin and modern evolution biology, however, scientists, including Darwin himself, began to understand that: "Our classifications will come to be, as far as they can be so made, genealogies; and will then truly give what may be called the plan of creation." Such genealogies are more usually called "phylogenies", using a word invented by Ernst Haeckel, a dedicated investigator of such arrangements. And the idea that taxa are to represent groupings defined by evolution has been an integral part of biology ever since.

Cladistics, invented by entomologist Willi Hennig in the 1950's, is the sort of rigorous application of the concept of evolution to taxonomy that Darwin envisioned. Phylogenies are established by what distinctive features their members share to the exclusion of more distantly related organisms. Thus, if one wants to identify some subgroup of insects, features that all insects have in common, like six legs and segmented bodies, are useless. One has to use features or combinations of features that only that subgroup has, like front wings becoming hard wing covers for Coleoptera (beetles) or scaly wings for Lepidoptera (butterflies and moths). One constructs phylogenies with this technique by trying to find the family tree that involves the fewest feature changes (steps), and thus the smallest amount of convergent evolution. Like phenetics, cladistics is almost always done by computer.

Groups are then delimited on this basis. Unlike the taxonomists of yore, phylogenetic taxonomists only recognize monophyletic groups; a group derived from a single common ancestor that contains all descendents of that ancestor. Thus, any definition of invertebrate that contains all forms without a notochord but not their descendants, i.e., those with a notochord, is seen as artificial and unscientific.

Evolutionary Taxonomy

Finally, traditional taxonomy is essentially a hybrid of these two, though sometimes a very subjective one. Traditional taxonomy has admitted numerous taxa that are cladistically illegitimate, because they exclude some of the descendants of the ancestors of their members. Such traditional taxa as Pisces, Reptilia, etc. are cladistically illegitimate, because legged vertebrates are descended from fish and birds from reptiles. "Evolutionary taxonomy" is essentially traditional taxonomy with evolution taken into account.

For the most part, hierarchy-based taxonomy has been very successful, but one-celled organisms often practice lateral gene transfer, and sometimes even lateral genome transfer (endosymbiosis), which cause difficulty for such taxonomies. In such cases, the "proper" taxonomies are those of genes or sets of genes, though as explained above, some genes serve as a reasonable proxy for the whole organism.

Creationist Taxonomy

Creationists have developed a concept of created kinds or "baramins" -- sets of species that share some specially-created ancestor. However, despite appropriating some cladistics jargon, they do not have any well-defined procedure for identifying baramins. As a result, they have great disagreements as to what baramins there are. Even worse, these disagreements are coupled with a curious lack of interest in resolving them, as mainstream scientists have often tried to do in similar circumstances.

Nomenclature

The criteria by which we group organisms is one thing; the manner in which we give them names, what those names mean and how we define them, is another. The approach to naming groups (nomenclature) most familiar to all of us was invented by Carl von Linné, (a.k.a. Carolus Linnaeus). He invented binomial nomenclature by snipping the then-often-used <genus> + <lots of attributes of a species> down to <genus> + <some distinctive attribute of a species>. He also rationalized nomenclature, using the same name for both sexes and for adults and juveniles of a species. Like many of his contemporaries, he used Latin, which has the useful feature of being nationalistically neutral since the fall of the Roman Empire.

His hierarchy of taxa (singular: taxon) was kingdom, class, order, genus, and species, but later taxonomists added phylum, division, family, lots of sub- and supertaxa, and even such taxa as domain, cohort, tribe, and section.

Taxonomic names and parts of names come from a variety of sources, though they must all be Latinized. Aside from personal and place names, taxonomic name parts are almost always words drawn from Latin and Classical Greek, with other languages occasionally represented. They are often common names (Homo, Canis, Bos, Equus, Columba, Salmo, Apis, Lilium, Rosa, Quercus, Pinus, etc.), and also words for various features and descriptions of them. Compound words are very common, though this sometimes leads to very long and difficult to pronounce names like Strongylocentrotus purpuratus (the purple sea urchin, found off the North American coast of the Pacific, often used as a model system). Higher-level taxa are often named after genera that they contain.

Several taxonomic ranks have standardized suffixes. Animal families end in -idae, plant families in -aceae, bird orders in -iformes, plant orders in -ales, etc. However, genera and lower-ranking taxa do not; genus names are singular nouns, while species names are either singular nouns, adjectives, or genitives (Latin's of-case). Also, taxon names above the genus are all plurals or collectives, whether or not they have some standardized suffix. Such conventions allow comparison of the ranks of different taxa at a glance.

Many organisms have received different names from different taxonomists; such conflicts are resolved by using the first-bestowed name. Thus, Apatosaurus pushed out Brontosaurus and Hyracotherium pushed out Eohippus. Although the international codes of nomenclature have no rules against it, this rule of priority has meant that some inappropriate names -- names that don't accurately reflect the content or characters of taxa -- have survived. The chimpanzee, Pan troglodytes, got its species name because Linnaeus had believed that it lives in caves; it actually lives in forests, making Pan silvanus more appropriate. Also, Basilosaurus ("king lizard") turned out to be an early cetacean rather than a marine reptile upon closer examination. The Venus Flytrap, Dionaea muscipula, might be more appropriately named something like Insecticaptrix muscipula or even Insecticaptrix carolinensis (Insect-taker/grabber (f., like planta), from Carolina).

Always Treelike?

An interesting conundrum is posed by organisms that have originated by symbiosis, since their phylogeny cannot be easily fit into a treelike topology. Lichens are the symbiosis of a fungus and an alga, which gives lichens that problem. But the fungus is more choosy about which alga than the alga about which fungus, meaning that lichen taxonomy follows that of their component fungi.

Related to this conundrum is organisms that have performed much lateral gene transfer, and sometimes even lateral genome transfer (endosymbiosis), as many one-celled organisms have done. In particular, the taxonomy of prokaryotes has traditionally been descriptive, because it has been difficult to work out their phylogeny without using molecular sequences. And if their molecules are all scrambled, as has been suggested, then one may be stuck with descriptive taxonomy. But the "average" molecular phylogeny approximates that of information-system macromolecules like often-used ribosomal RNA. So as with lichens, a treelike phylogeny-based taxonomy remains reasonable when one uses some reasonable subset of the organism.

PhyloCode

Because of the various problems with standard Linnaean taxonomy and nomenclature, some researchers have instead advocated a radical cladistics-based approach known as PhyloCode (see http://www.ohiou.edu/phylocode/ and http://en.wikipedia.org/wiki/PhyloCode); however, many other researchers feel the PhyloCode approach is clumsy, awkward, and throws out the proverbial baby with the proverbial bathwater (see http://www.systass.org/archive/events-archive/2001/phylocode-debate.shtml ).

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