When the APG II system of plant classification was published in April 2003, fifteen genera and three families were placed incertae sedis in the angiosperms, and were listed in a section of the appendix entitled "Taxa of uncertain position".
[1] By the end of 2009, molecular phylogenetic analysis of DNA sequences had revealed the relationships of most of these taxa, and all but three of them had been placed in some group within the angiosperms.
Cynomorium was raised to familial status as Cynomoriaceae, and along with Apodanthaceae and Gumillea, remained unplaced in APG III.
There is no apparent reason for the inclusion of Leptaulus in the list of unplaced taxa, other than the time lag between submission and publication.
In 2001, in a phylogenetic study based on morphological and DNA data, Leptaulus was found to belong to a group of six genera that most authors now consider to be the family Cardiopteridaceae.
Instead, they segregate Cardiopteris into a monogeneric Cardiopteridaceae sensu stricto and place the other five genera in the family Leptaulaceae.
[citation needed] It had long been thought, at least by some, that the small Southeast Asian tree Pottingeria might belong in the order Celastrales.
It was in an unresolved pentatomy consisting of Parnassiaceae, Pottingeria, Mortonia, the pair (Quetzalia + Zinowiewia), and the other genera of Celastraceae.
[7] When the APG III system was published in October 2009, the Angiosperm Phylogeny Group expanded Celastraceae to include all members of the pentatomy mentioned above.
[10] In 2009, in a molecular phylogenetic study of the order Huerteales, it was shown that Dipentodon and Perrottetia belong together as the two genera of the family Dipentodontaceae.
[11] In 2009, in a molecular phylogenetic study of Malpighiales, Kenneth Wurdack and Charles Davis sampled five genera and one family that had been unplaced in APG II.
[13] Wurdack and Davis also found that the family Rafflesiaceae and the genera Aneulophus, Centroplacus, and Trichostephanus belong in the order Malpighiales.
[citation needed] The relationships of some parasitic taxa have been elucidated in studies of nuclear and mitochondrial DNA sequences.
But these sequences sometimes produce artifactual topologies in the phylogenetic tree, because horizontal gene transfer often occurs between parasites and their hosts.
[17] The parasitic genera Bdallophyton and Cytinus have been found to be closely related and have been placed together as the family Cytinaceae.
[19] A phylogeny based on mitochondrial genes places Mitrastemon in the order Ericales, but this result had only 76% maximum likelihood bootstrap support.
[20] Attempts to find its closest relatives have demonstrated with special clarity that molecular phylogenetics is not a sure-fire, problem-free method of determining systematic relationships.
[36] George Bentham and Joseph Hooker placed it in Cunoniaceae,[37] and this treatment was followed by Adolf Engler and most others.
[42][43] It is worth noting that on their plate for Gumillea, Ruiz and Pavón showed 11 ovules or immature seeds that had been extracted from a 2-locular ovary.
[45] Attempts to determine the relationships of Apodanthaceae have produced only uncertain results and they have remained enigmatic,[20][46] until the family was shown to be confidently placed in Cucurbitales[47]