When theAPG II system ofplant classification was published in April 2003, fifteengenera and threefamilies were placedincertae sedis in theangiosperms, and were listed in a section of the appendix entitled "Taxa of uncertain position".[1]
By the end of 2009,molecular phylogenetic analysis ofDNA sequences had revealed therelationships of most of thesetaxa, and all but three of them had been placed in somegroup within the angiosperms. In October 2009, APG II was superseded by theAPG III system.[2] In APG III, 11 of the genera listed above were placed in families, or else became families whose position within their orders was approximately or exactly known. The family Rafflesiaceae was placed in theorderMalpighiales, close toEuphorbiaceae and possibly within it.Mitrastema became amonotypic family, Mitrastemonaceae. This family and Balanophoraceae were placedincertae sedis into orders, that is, their positions within these orders remained completely unknown.Metteniusa was found to belong to asupraordinal group known as thelamiids, which has not been satisfactorily divided into orders.Cynomorium was raised to familial status as Cynomoriaceae, and along with Apodanthaceae andGumillea, remained unplaced in APG III. Five taxa were unplaced among the angiosperms in APG III becauseNicobariodendron andPetenaea were added to the list.
There is no apparent reason for the inclusion ofLeptaulus in the list of unplaced taxa, other than the time lag between submission and publication. In 2001, in a phylogeneticstudy based onmorphological andDNA data,Leptaulus was found to belong to a group of six genera that most authors now consider to be the familyCardiopteridaceae.[3] This was confirmed in a study ofwoodanatomy in 2008.[4] The genus is placed in the Cardiopteridaceae in theAPG III system of 2009.[1] Before 2001,Leptaulus and the rest of Cardiopteridaceae had usually been placed in a broadlycircumscribedIcacinaceae, which turned out to bepolyphyletic.[citation needed]
Some botanists do not recognize Cardiopteridaceae as a family of six genera. Instead, theysegregateCardiopteris into amonogeneric Cardiopteridaceaesensu stricto and place the other five genera in the family Leptaulaceae.[5] Themonophyly of Leptaulaceae has never been tested with molecular data.[citation needed]
It had long been thought, at least by some, that the smallSoutheast Asian treePottingeria might belong in the orderCelastrales.[6] In a phylogenetic study of that order in 2006,Pottingeria was found to be a member of the order, but not of any of its families. It was in an unresolvedpentatomy consisting ofParnassiaceae,Pottingeria,Mortonia, the pair (Quetzalia +Zinowiewia), and the other genera ofCelastraceae.[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.[8]
Dipentodon has one speciesDipentodon sinicus.[9] It isnative to southernChina,Burma, and northernIndia.[10] In 2009, in a molecular phylogenetic study of the orderHuerteales, it was shown thatDipentodon andPerrottetia belong together as the two genera of the familyDipentodontaceae.[11]
In 2009, in a molecular phylogenetic study ofMalpighiales, Kenneth Wurdack and Charles Davis sampled five genera and one family that had been unplaced in APG II. They placed some of these for the first time and confirmed the previous placement of others with strongstatistical support.[12]
In theiroutgroup, they included four genera fromSaxifragales. These wereDaphniphyllum,Medusandra,Soyauxia, andPeridiscus. In their phylogeny,Medusandra andSoyauxia formed a strongly supportedclade withPeridiscus, a member of the familyPeridiscaceae, the mostbasal clade in Saxifragales. Wurdack and Davis recommended thatMedusandra andSoyauxia both be transferred to Peridiscaceae. Thus the monogeneric family Medusandraceae is subsumed into Peridiscaceae.Soyauxia had been found to be close toPeridiscus in another study two years before.[13] Wurdack and Davis also found that the family Rafflesiaceae and the generaAneulophus,Centroplacus, andTrichostephanus belong in the order Malpighiales.[12]
Aneulophus consists of two species ofwoody plants fromtropicalWest Africa.[14] Wurdack and Davis found the traditional placement ofAneulophus inErythroxylaceae to be correct.[12] Its position within the family remains uncertain.[citation needed]
Erythroxylaceae is a family of four genera.Erythroxylum has about 230 species.Nectaropetalum has eight species andPinacopodium has two. No one has yet produced a molecular phylogeny of the family.[citation needed]
Centroplacus has a single species,Centroplacus glaucinus, a tree from West Africa. It was found to be close toBhesa, a genus that had only recently been removed from Celastrales.[7]Bhesa was grouped withCentroplacus to become the second genus in Centroplacaceae.[12]Bhesa consists of five species of trees fromIndia andMalesia.
Trichostephanus has two species, both in tropical West Africa. It had usually been assigned toAchariaceae, but it was found to be deeply embedded inSamydaceae.[12][15] Manytaxonomists do not recognize Samydaceae as a separate family fromSalicaceae.[citation needed]
Several genera have been removed from Rafflesiaceae, so that it now consists of only three genera:Sapria,Rhizanthes, andRafflesia. All of these areholoparasites and, as discussed below, finding their relationships by molecular phylogenetics has presented special challenges.Rafflesia and its relatives were the subject of several papers from 2004 to 2009, and as the world's largest flower,Rafflesia has attracted special interest. In 2009, Wurdack and Davis confirmed earlier work in which it was found that Rafflesiaceae is nested withinEuphorbiaceaesensu stricto, a circumscription of Euphorbiaceae that excludesPhyllanthaceae,Picrodendraceae,Putranjivaceae,Pandaceae, and a few other very small groups that had been included in it until the 1990s.[16] In order to preserve Rafflesiaceae, Wurdack and Davis split Euphorbiaceae sensu stricto into Euphorbiaceaesensu strictissimo andPeraceae, a new family comprisingPera and four other genera.[12]
Four of the unplaced genera, and all three of the unplaced families of APG II consist ofachlorophyllousholoparasites. In these, thechloroplastgenes that are usually used in phylogenetic studies of angiosperms have become nonfunctionalpseudogenes. If theseevolve rapidly, they may be saturated with repeatedmutations at the same site and consequently not be useful for phylogenetic reconstruction.[citation needed]
The relationships of some parasitic taxa have been elucidated in studies ofnuclear andmitochondrial DNA sequences. But these sequences sometimes produceartifactualtopologies in thephylogenetic tree, becausehorizontal gene transfer often occurs between parasites and theirhosts.[17]
The parasitic generaBdallophyton andCytinus have been found to be closely related and have been placed together as the familyCytinaceae. On the basis of mitochondrial DNA, Cytinaceae has been placed inMalvales, assister toMuntingiaceae.[18]
The parasitic family Mitrastemonaceae has one genus, known either asMitrastemon orMitrastema. The genus name and the corresponding family name have been a source of much confusion.[19] A phylogeny based on mitochondrial genes placesMitrastemon in the orderEricales, but this result had only 76%maximum likelihoodbootstrap support.[20]
Hoplestigma consists of two species ofAfrican trees, notable for their large leaves, up to 55 cm long and 25 cm wide.[21] It is usually placed by itself in the family Hoplestigmataceae which is thought to be related toBoraginaceae.[22] In 2014, a phylogeny of Boraginaceae waspublished in ascientific journal calledCladistics.[23] By comparing theDNA sequences of selectedgenes, the authors of thatstudy showed thatHoplestigma is related to members of BoraginaceaesubfamilyCordioideae, and they recommended thatHoplestigma be placed in that subfamily. Other authors have suggested that, whileHoplestigma is theclosest relative of Cordioideae, it should perhaps not be placed within it.[24]
Metteniusa consists of seven species of trees inCentral America and northwesternSouth America. Ever sinceHermann Karsten proposed the name Metteniusaceae in 1859, some authors have placedMetteniusa by itself, in that family.[25] Most authors, however, placed it inIcacinaceae until that family was shown to be polyphyletic in 2001.[3]
In 2007, in a comparison of DNA sequences for three genes, it was found thatMetteniusa is one of thebasal clades of thelamiids. The authors recommended that the family Metteniusaceae be recognized.[26] Nothing is yet known about relationships among the groups of basal lamiids. Thegroups in thispolytomy include the orderGarryales, the familiesIcacinaceae,Oncothecaceae, andMetteniusaceae, as well as some unplaced genera, includingApodytes,Emmotum, andCassinopsis.[24]
No phylogenetic study has focused on the lamiids, but phylogenies have been inferred for theasterids, a group composed ofCornales,Ericales, thelamiids, and thecampanulids.[27][28]
Balanophoraceae is a family of holoparasites with 44 species in 17 genera.[24] For a long time,Cynomorium was usually included in this family, but it is now known to be unrelated.[20] In 2005, Balanophoraceae was shown to be in the orderSantalales, but its position within that order has not been determined.[29]
Two researchers inTaiwan announced on the internet in 2009 that they have results supporting the placement of Balanophoraceae in Santalales.[30] They have yet to publish anything in ascientific journal.[citation needed]
Many names have been published inCynomorium,[31] but there are probably onlytwo species.[32] It is not closely related to anything else, so it is placed in the monogeneric family Cynomoriaceae.[20]
Attempts to find its closest relatives have demonstrated with special clarity that molecular phylogenetics is not a sure-fire, problem-free method of determiningsystematic relationships. One study placed it in Saxifragales, but not at any particular position within that order.[29] Doubts have been expressed about the results of this study. Another study placedCynomorium inRosales based on analysis of the twoinvert repeat regions of the chloroplastgenome, which evolve at one fifth therate of the twosingle copy regions.[33]
Gumillea has a single species,Gumillea auriculata,[34] and is known from only onespecimen which was collected in the late 18th century inPeru.[35] It was named byHipólito Ruiz López andJosé Antonio Pavón Jiménez.[36]
George Bentham andJoseph Hooker placed it inCunoniaceae,[37] and this treatment was followed byAdolf Engler and most others.[34] The last comprehensive treatment of Cunoniaceae, however, excludes it from the family.[38] In 2009,Armen Takhtajan placedGumillea inSimaroubaceae.[39] A 2007 article on Simaroubaceae contains a list of the genera in the family.Gumillea is not on that list, but the authors do not provide a list or section on excluded genera.[40]
Gumillea has also been called asynonym ofPicramnia,[14][41] but the ultimate source of this information is obscure and it is not mentioned in either of the recent treatments ofPicramnia.[42][43] It is worth noting that on theirplate forGumillea, Ruiz and Pavón showed 11ovules or immatureseeds that had been extracted from a 2-locularovary. But the ovary inPicramnia has (sometimes 2), usually 3 to 4 locules and there are always two ovules in each locule.[43]
It might be possible to determine the affinities ofGumillea if DNA could be extracted from the existing specimen. DNA has been successfullyamplified from specimens of similar age.[44] Any material used in such research, however, will never be replaced.
The family Apodanthaceae comprises 22 to 30 species ofendoparasiticherbs. These are distributed into three genera:Pilostyles,Apodanthes, andBerlinianche.[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]