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Although known in antiquity, Pier Antonio Micheli's was the first to study them in detail and included them in his 1729 work Nova plantarum genera, however he still considered them to be plants. Christian Hendrik Persoon established the first classification of mushrooms and is considered a founder of modern mycology.

In 1969, an American biologist, Robert Harding Whittaker, recognised that fungi are very different from other eukaryotes in many essential aspects, so he designated them to a new kingdom. Whittaker's clarification of the system attempted to place organisms in kingdoms that more nearly resembled their supposed evolutionary relationships. This five kingdom approach to classifying organisms was an important step in the attempt to form groups that contain an ancestor and all its descendants (monophyletic groups) and to create a system where similarities and relationships may be seen. It had long been accepted that evolution had occurred since the publication of The Origin of Species(Darwin, 1859); where present species had evolved from earlier species and where similar species had a recent common ancestor, different species a more distant one. Thus a natural classification should mirror descent. Whittaker noticed, for example, the methods of nutrient intake for the three main eukaryote kingdoms (Animals, plants and fungi) were completely different. Animals absorb nutrients internally, engulfing food by the action of ingestion. Plants too have a form of internal absorption, with the intake of energy from the sun by photosynthetic organelles (Chloroplasts). Fungi, however, are the only eukaryote who have to externally digest their food component prior to absorption. Characteristically, fungi dwell in a food source absorbing nutrients from the medium, and in many instances releasing digestive enzymes for external digestion. In the last 30 years, recent advancements in technology, including DNA sequencing techniques, have placed a severe strain on Whittaker's five-kingdom system. At present, the dispute of the number of kingdoms required to classify all living and fossil taxa still is not concluded. Kingdoms are really the trunk and major branches of an evolutionary tree. Splitting the tree into kingdoms is an arbitrary process and depends whereabouts along the trunk and branches you make your cut. The higher you cut, the more kingdoms you will get. In fact some of the classification schemes which have been brought forward contain more than 15 kingdoms! A five-kingdom system of life has a charming simplicity. Unfortunately, throughout evolution, many losses and births of complex characters entangle this system. Therefore, down to molecular sequencing in particular, a six-kingdom system now seems necessary to enable us to place organisms in a fairer and more defined phylogenetic classification.

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