Monophyletic

It has been suggested that paraphyly and polyphyly be merged into this article or section. (Discuss)

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A clade is a taxonomic group (such as one of organisms) comprising a single common ancestor and all the descendants of that ancestor. Any such group is considered to be a monophyletic group, and can be represented by both a phylogenetic analysis, as in a tree diagram, and by a cladogram (see cladistics), or simply as a taxonomic reference.

The grouping of reptiles and birds is generally believed to be monophyletic.

Main article: Cladistics

If a clade proves robust in alternate cladistic analyses using different sets of data, it may be adopted into taxonomy and become a taxon. Not all taxa, however, are considered to be clades. Reptiles, for example, are a paraphyletic group because they do not include aves (birds), which are thought to also have evolved from the common ancestor of the reptiles.

In cladistics, a clade that is located within another more inclusive clade is said to be "nested" within that clade. Nested clade analysis is beneficial in many ways. For instance, it enables the detection of range expansions in isolated geographic areas.

Contents 1 Phylogenetic nomenclature 2 Traditional binomial nomenclature 3 Relation to paraphyletic and polyphyletic groups 4 Phylogenetic alternatives 5 External links

Phylogenetic nomenclature

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Phylogenetic nomenclature is formulated in terms of evolution and common descent rather than the type specimens, categorical ranks, and morphological characters. The latter is used most commonly in cladistic analysis. Taxon names are strictly connected to phylogenetic tree topology and evolutionary history. In taxonomy, each name is attached to a clade taxonomic group containing a common ancestor and all its descendants. Phylogenetic nomenclature discards categorical ranks. The problem with ranks are evident when one considers biodiversity lineages and clades. Questions like "how many lineages are there?" or "how many clades are there?" become pointless, since there are no answers. These are relative concepts, illustrating the fractal nature of the tree of life and the need to let a phylogenetic hypothesis be the focus, rather than the categories, when biodiversity is quantified. Phylogenetic nomenclature helps to put focus on phylogenetic trees by offering an explicit link between names and parts of species history, that is, clades.

Traditional binomial nomenclature

In phylogenetics, binomial names are associated with the relationships of each described species. But this creates a problem because it makes assumptions about relationships about the description of the species identification. It suggests that species or genera are a unique category, and this contradicts the idea of recognizing only clades and lineages.

Relation to paraphyletic and polyphyletic groups

Paraphyletic Group

Polyphyletic Group

Groups that do not include all the descendants of the most recent common ancestor are said to be paraphyletic. For example, as shown in the adjacent illustration, reptiles are paraphyletic because that group excludes birds. A group that does not contain the most recent common ancestor of its members is said to be polyphyletic (Greek polys = many). An example of a polyphyletic group is the warm-blooded animals.

Phylogenetic alternatives

To avoid the pitfalls of traditional Linnaean taxonomy in phylogenetic nomenclature, three new methods of phylogenetic naming have been proposed: node-, stem-, and apomorphy-based. In node-based naming, taxon name A might refer to the least inclusive clade containing X and Y. In stem-based naming, A would refer to the most inclusive clade containing X and Y but not Z. In apomorphy (derived feature)-based naming, A would refer to the clade identified by a feature synapomorphic (sharing a derivation) with a feature in specimen (taxon) X. Differences between a traditional approach and these phylogenetic alternatives become obvious when the phylogenetic hypothesis changes. Comparison between the traditional Linnaean approach to nomenclature and a phylogenetic alternative (node-based naming). Suppose that all we want to do is to give a name ("A") to a clade containing X and Y. In the Linnaean system this means that we have to introduce names for sister taxa, assigning all taxa to the categories species, genus, and family, and designate type species. No explicit reference to phylogeny is made. The phylogenetic alternative provides an explicit reference to evolutionary history, and nothing but the clade containing X and Y needs to be named. When the hypothesis of relationship changes, the phylogenetic alternative is cleaner and more explicit about what it refers to.

v • d • e Topics in phylogenetics
Relevant fields	Computational phylogenetics · Molecular phylogeny · Cladistics
Basic concepts	Synapomorphy · Phylogenetic tree · Phylogenetic network · Long branch attraction
Inference methods	Maximum parsimony · Maximum likelihood · Neighbor-joining · UPGMA · Bayesian inference · Least squares
Current topics	PhyloCode · DNA barcoding
List of evolutionary biology topics

v • d • e Basic topics in evolutionary biology
Evidence of evolution
Processes of evolution	Adaptation · Macroevolution · Microevolution · Speciation
Population genetic mechanisms	Natural selection · Genetic drift · Gene flow · Mutation
Evolutionary developmental biology (Evo-devo) concepts	Phenotypic plasticity · Canalisation · Modularity
The evolution of...	DNA · Sex · Aging · Intelligence · The Ear · The Eye · Flight · Plants · Fungi · Animals · Homo sapiens
Modes of speciation	Anagenesis · Catagenesis · Cladogenesis
History	History of evolutionary thought · Charles Darwin · On the Origin of Species · Modern evolutionary synthesis · Gene-centered view of evolution · Evolutionary history of life · Life (classification trees)
Other subfields	Ecological genetics · Human evolution · Molecular evolution · Phylogenetics · Systematics
List of evolutionary biology topics · Timeline of evolution

External links

• Evolving Thoughts: Clade
• A poster-sized cladogram showing the Tree of Life (Evolution)
• DM Hillis, D Zwickl & R Gutell: ~3000 species Tree of Life A cladogram?
• Phylogenetic systematics, an introductory slide-show on evolutionary trees University of California, Berkeley

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