Editing Linnaean taxonomy (section)

=== Alternatives ===
Over time, understanding of the relationships between living things has changed. Linnaeus could only base his scheme on the structural similarities of the different organisms. The greatest change was the widespread acceptance of [[evolution]] as the mechanism of biological diversity and species formation, following the 1859 publication of Charles Darwin's ''[[On the Origin of Species]]''. It then became generally understood that classifications ought to reflect the [[phylogeny]] of organisms, their descent by evolution. This led to [[evolutionary taxonomy]], where the various [[extant taxon|extant]] and [[extinction|extinct]] are linked together to construct a phylogeny. This is largely what is meant by the term 'Linnaean taxonomy' when used in a modern context.
In [[cladistics]], originating in the work of [[Willi Hennig]], 1950 onwards, each taxon is grouped so as to include the common ancestor of the group's members (and thus to avoid [[phylogeny]]). Such taxa may be either [[monophyly|monophyletic]] (including all descendants) such as genus ''[[Homo]]'', or [[paraphyly|paraphyletic]] (excluding some descendants), such as genus ''[[Australopithecus]]''.

Originally, Linnaeus established three kingdoms in his scheme, namely for [[Plant]]s, [[Animal]]s and an additional group for [[minerals]], which has long since been abandoned.  Since then, various life forms have been moved into three new kingdoms: [[Monera]], for [[prokaryote]]s (i.e., bacteria); [[Protist]]a, for protozoans and most algae; and [[fungus|Fungi]].  This five-kingdom scheme is still far from the [[phylogenetics|phylogenetic]] ideal and has largely been supplanted in modern taxonomic work by a division into three domains: [[Bacterium|Bacteria]] and [[Archaea]], which contain the prokaryotes, and [[Eukaryote|Eukaryota]], comprising the remaining forms. These arrangements should not be seen as definitive. They are based on the [[genome]]s of the organisms; as knowledge on this increases, classifications will change.<ref>{{cite journal|author1=Embley, T. A.  |author2=Martin, W. |name-list-style=amp|date=2006 |title=Eukaryotic evolution, changes and challenges. |journal=Nature |volume=440 |issue=7084 |pages=623–630 |doi=10.1038/nature04546 |pmid=16572163 |s2cid=4396543 |url=http://www.nature.com/scitable/content/eukaryotic-evolution-changes-and-challenges-13997647|url-access=subscription }}</ref>

Representing presumptive evolutionary relationships within the framework of Linnaean taxonomy is sometimes seen as problematic, especially given the wide acceptance of [[cladistic]] methodology and numerous [[molecular phylogenetic|molecular phylogenies]] that have challenged long-accepted classifications. Therefore, some systematists have proposed a [[PhyloCode]] to replace it.