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Characters shared by a group of taxa due to descent from a most recent common ancestor (i.e., synapomorphies) constitute the evidence to support the nested structure of a given cladogram.
Homology is basically similarity due to descent of information from a common ancestor to its descendants, and sharing homologous similarities may signal unique ancestry or it may signal more ancient ancestry.
Phylogenetic signal is a tendency for closely related taxa to possess similar trait values due to descent from a common ancestor.
These longer n-mers should only be shared between species due to descent from a common ancestor.
Using Figure 1a as an example, one might suggest taxon F is closely related to taxon C (which is true), because taxon F is descended from taxon C. Taxon F and taxon C are not closely related because one extant taxa is descended from the other, but rather due to descent from a recent common ancestor.
Similar(55)
When we used phylogenetic models that control for similarity between species, due to common descent, and focused on variations within a single lineage (DRB1*03), the positive relationship between different substitution rates and allelic polymorphisms was still robust.
Their skeletal structure is homologous, due to common descent from the forelimb of a reptilian ancestor; but the modifications for flying are different and independently evolved, and in this respect they are analogous.
On this hypothesis, the code arose only once, and the coincidence is due to common descent.
When there are reasons to think that the model and the target share similar causal mechanisms due to common descent, Steel's "extrapolator's circle" may not arise.
The posterior fossa deformity can also be seen: the cisterna magnum is absent and the foramen magnum is enlarged due to the descent of the structures of the posterior fossa toward the spinal canal (arrows in b).
Characters that are consistent with the ensemble cladogram can then be classified as homologous (i.e. similarities due to common descent) while those that are inconsistent with it can be classified as homoplastic (i.e. similarities that are due to other processes, such as borrowing and blending among lineages).
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