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In cladistics, a synapomorphy or synapomorphic character state is a trait that is ancestral and inferred to have been present in their most distant common ancestor  A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question is assumed to have originated in their oldest common ancestor. The word "synapomorphy," coined by German entomologist Willi Hennig, is derived from the Greek words σύν, syn = with, in company with, together with; ἀπό, apo = away from; and μορφή, morphe = shape.
For the sake of precision, the term "primative" is preferred to "simple". Simplicity is often secondarily derived. For example, the absence of mitochondria in the anaerobic protist Entamoeba histolytica is a result of their secondary loss, and when considered in the context of eukaryotes as a whole, is a derived trait. Likewise, the primitive character state for birds (i.e. the state possessed by their last common ancestor) is flight, which was secondarily lost by penguins and dodos.
Whether or not a trait is considered derived depends on the group in question. For example, among the (crown group) tetrapods, having five fingers is the primitive trait - as their last common ancestor bore a five-digit hand. However, amongst the vertebrates, five fingers is a derived trait, as the last common ancestor to the vertebrates did not even bear fingers.
Comparisons with other convergent traits
A synapomorphy should not be confused with other types of shared traits:
- A synapomorphy is a convergent trait found among two or more taxa and inferred to have occurred in their most recent common ancestor, whose ancestor in turn did not possess the trait. An example is the dipteran halteres, the uniquely modified hind wings found in all families of winged flies. No other group of insects possesses similar structures (in place of hind wings—insects in the order Strepsiptera have convergently-evolved halteres in place of fore wings). However, the fact that the trait is found only in Diptera, to the exclusion of all other groups, is not essential in identifying the trait as a synapomorphy; rather, this fact makes its determination easier. (However, among dipteran insects there are forms, which lack both fore and hind wings completely, for instance, Braula and Melophagus).
- A symplesiomorphy is a shared trait found among two or more taxa, but which is also found in taxa that are related only through a more remote common ancestor (symplesiomorphy characterizes a paraphyletic group). An example of this is the five toes seen on the hind legs of rats and apes. This character-state originated very early in Tetrapoda and occurs in other tetrapod groups, e.g. in salamanders, lizards and lemurs. There is thus no indication that the group formed of rats and apes is a clade to the exclusion of these other groups; indeed, although rats and apes are much more closely related to each other than they are to salamanders or lizards (as they are both mammals of the clade Euarchontoglires), apes are even more closely related lemurs than they are to rats (both apes and lemurs are primates, a clade within Euarchontoglires). From this example, it is evident that a symplesiomorphy is a synapomorphy for a group of greater generality (Tetrapoda, in this instance).
- A homoplasy is a shared trait found among different taxa but inferred to have been independently derived and not to have occurred in their common ancestor (i.e., a trait considered to be "the same" emerged in different taxa independently of each other). An example of this is homeothermy in birds and mammals. This trait is a derived character-state (in relation to poikilothermy, the character-state inferred to have been that of the last common ancestor of both groups), which therefore is hypothesized to have evolved independently in these two groups (or at least in the larger clades to which these groups belong). Homoplasy can only be discovered by incongruence of the homoplastic character states with respect to the weight of other evidence in a phylogenetic analysis.
Synapomorphies are used to establish phylogenetic hypotheses in cladistic analysis. As such they are empirical data which can support a certain hypothesis that terminal groups form a clade (monophyletic group) together to the exclusion of certain other groups – whereas character-states that are shared, but also shared by other terminal groups descending from an earlier common ancestor, cannot be used to exclude these other groups. The latter character-states can consist of symplesiomorphies ("primitive" character-states inferred to have originated in an earlier common ancestor) or homoplasies (features that are superficially similar but, based on the weight of evidence are inferred to have been independently evolved derived character-states).
The key problem is to identify the polarity of the transformation series to which several character-states belong, i.e. to tell which character-state is apomorphic and which is plesiomorphic. Various criteria were used to polarize transformation series in earlier cladistics; however in recent decades pattern criteria based on outgroup comparison have dominated the field. An outgroup is a taxon assumed to be outside of the group of interest in the study. Under the outgroup criterion, character states shared between the outgroup and some members of the ingroup are inferred to be plesiomorphic, while alternative states of the same feature that are shared by a subset of the ingroup are considered to be apomorphic.
The concepts of apomorphy and plesiomorphy are relative to a certain level of generality in the hierarchy of life. What counts as an apomorphy at one level of generality may well be a plesiomorphy at a less inclusive level. For example, the presence of mammary glands is a synapomorphy for mammals in relation to tetrapods more broadly, but is a symplesiomorphy for mammals in relation to one another, e. g., rats and apes.
It is not essential that all members of a clade possess exhibit a synapomorphy; even if some members of the clade have secondarily lost the trait it could still be a synapomorphy of the clade as a whole. A good example of this is the "absence" of legs in snakes, which are nevertheless members of Tetrapoda. Among paleontologists, a character state that is a synapomorphy for a clade, but for lineages in this clade is a plesiomorphy that is altered in some lineages, is called an underlying synapomorphy. If no crown group taxa are known, it is sometimes difficult to decide which character state is the underlying synapomorphy and which the autapomorphy that overlies it.
Clades are not defined by synapomorphies as such, though it is possible to define them by apomorphies in general.
Relative apparent synapomorphy analysis is a method that some use to determine whether a given character is shared between taxa due to shared ancestry or due to convergence.
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