Although the Jurassic troodontid Anchiornis has been recently demonstrated to have egested pellets similar to extant carnivorous birds (most famously documented in owls), this ability was apparently absent in Microraptor, further adding to the evidence that the evolutionary transition from dinosaur to bird was characterized by extreme
homoplasy - that is, numerous traits evolved multiple times independently in closely related groups.
Cell lineages appear to be unreliable indicators of homology or
homoplasy of metatrochs.
The Index of Consistency (IC) was of 0.73, Index of
Homoplasy (IH) of 0.26, Index of Retension of 0.67 and Index of Re-phased Retension of 0.49.
Thus, if the new species belongs to Pikelinia, the presence of an unfused cymbium would represent at least one instance of
homoplasy. On the other hand, the new species shows a particular shape of the cymbium: large, anteriorly convex, covering the bulb dorsally, and with an area devoid of setae.
What remains unclear is whether this group is monophyletic or simply a case of
homoplasy among hominins.
The Pairwise
Homoplasy Index (PHI) test for recombination was conducted with the SplitsTree v.4.10 following the default settings [38].
The use of a high number of MIRU-VNTR loci also reduces the likelihood of
homoplasy. Furthermore, although the biological clock of the MIRU-VNTR marker seems to be relatively stable (recently estimated MIRU-VNTR mutation rate for TB is 2.70 x 10-3 mutations/ locus/year [15]), changes accruing in the marker could lead to misclassification of clonal strains as polyclonal strains; we used the ClassTR method in an attempt to minimize such misclassification.
For example, the higher level relationships of Sonorelix and Sonorella have been studied and discussed in depth due to their similarity in reproductive structure, but there is no consensus on whether they are both simplified due to
homoplasy or are closely related in lineage (Miller and Naranjo-Garcia 1991, Roth 1996).
This approach, which weights characters during searches according to their
homoplasy, has shown to enhance the results of morphological data analyses when compared with equal-weighted parsimony (see discussion in Goloboff et al., 2008b).
However, if microsatellite similarities were due to
homoplasy instead of true identity-by-descent, we would not be able to detect evolutionary differences using these methods, which could possibly result in putative subspecies that are less-similar than reported here (Garza and Freimer, 1996).
Finally, 1 locus, Ccmic9, showed evidence of allelic
homoplasy.
Data from amplified fragment length polymorphism (AFLP) markers show indication of size
homoplasy and of a relationship between degree of
homoplasy and fragment size.