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Taxonomy is the science of classifying, naming, and describing organisms. Taxonomy is a part of the scientific practice known as systematics, which entails the evolutionary relationships between organisms. The most prevalent naming system is the Linnaeus system, which is binomial system of nomenclature. This system uses two words to classify an organism’s species: genus and specific epithet. These two words are listed in italics or underlined in scientific documents. The typical classification system goes from broadest to narrowest as follows: kingdom, phylum, class, order, family, genus, species.
In taxonomy, evolutionary relationships are used in order to classify organisms, however, there are several different methods of classification. In any of these methods of classification, a taxon, or group of organisms, can be specified in several different ways. A monophyletic group is one which contains all of the descendants of a common ancestor, a paraphyletic group is one which contains some of he descendants of a common ancestor, but not all, and a polyphyletic group has many different evolutionary lines which don’t have a common ancestor. Kingdom Protista is an example of a polyphyletic group, for biological purposes, such a taxon classification leads to inaccuracy, for the organisms are often not related.
In order to determine evolutionary relationships, different characters are analyzed. Using outgroup analysis, a group of three species, which are thought to be related are examined. If a character is present in two of the three species, then the character is said to be a synapomorphic character. If the character is present in all of the three species, then the character is said to be a pleisomorphic character.
Another method of classification is molecular taxonomy. In molecular taxonomy, proteins and genes are used to determine evolutionary relationships. The percent of DNA which is similar in species is taken into consideration. Signature sequences are also used to determine between different prokaryotes, a signature sequence is the rRNA in a organism. Once a species has been carefully examined, specific genes or proteins can be used as molecular clocks, which determine the divergence from a common ancestor.
There are two main approaches to classifying organisms based on their shared and ancestrial characters. Phylogenetic systematics is one which emphasizes the shared, or synapomorphic characters. When any systematics is done properly, it must be assured that the characters being analyzed are homologous and not homoplastic. A homologous character derived from the same ancestor, while a homoplastic character derived from different ancestors to complete the same end function. The second classification approach is classical evolutionary taxonomy, which takes into account shared (synapomorphic) and ancestrial (pleisomorphic) characters. This approach is more accurate for it not only shows the evolutionary branching, but it shows divergence, which allows for a better understanding of the relationships.
Many years ago, phenetics, also known as numerical taxonomy, was used in order to classify organisms. This entailed quantifying the number of shared behaviors, and anatomical parts between species. The only problem with this is that they compared homologous characters to homoplastic characters which did not show evolutionary relationships.
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