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The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being).Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
The term sister group is used in phylogenetic analysis, however, only groups identified in the analysis are labeled as "sister groups".. An example is birds, whose commonly cited living sister group is the crocodiles, but that is true only when discussing extant organisms; [3] [4] when other, extinct groups are considered, the relationship between birds and crocodiles appears distant.
The formula of the definition indicates an ancestor. The defined taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically defined taxon relies on a phylogenetic hypothesis. The following are examples of types of phylogenetic definition (capital letters indicate specifiers): [11]
Early phylogenetic tree by Haeckel, 1866. Groups once thought to be more advanced, such as birds ("Aves"), are placed at the top. The idea of a clade did not exist in pre-Darwinian Linnaean taxonomy, which was based by necessity only on internal or external morphological similarities between organisms.
An example of a long-established taxon that is not also a clade is the class Reptilia, the reptiles; birds and mammals are the descendants of animals traditionally classed as reptiles, but neither is included in the Reptilia (birds are traditionally placed in the class Aves, and mammals in the class Mammalia).
The basal position is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. A basal clade is the earliest clade (of a given taxonomic rank[a]) to branch within a larger clade.
The results are a phylogenetic tree—a diagram setting the hypothetical relationships between organisms and their evolutionary history. [4] The tips of a phylogenetic tree can be living taxa or fossils, which represent the present time or "end" of an evolutionary lineage, respectively. A phylogenetic diagram can be rooted or unrooted.
A cladogram of the primates, showing a monophyletic taxon: the simians (in yellow); a paraphyletic taxon: the prosimians (in cyan, including the red patch); and a polyphyletic group: the night-active primates, i.e., the lorises and the tarsiers (in red). A cladogram of the vertebrates showing phylogenetic groups.