Unplaced in APG II
Encyclopedia
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".
By the end of 2009, molecular phylogenetic analysis of DNA sequence
s had revealed the relationships
of most of these taxa
, and all but three of them had been placed in some group
within the angiosperms. In October 2009, APG II was superseded by the APG III system
. 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 the order
Malpighiales
, close to Euphorbiaceae
and possibly within it. Mitrastema became a monotypic family, Mitrastemonaceae. This family and Balanophoraceae were placed incertae sedis into orders, that is, their positions within these orders remained completely unknown. Metteniusa was found to belong to a supraordinal
group known as the lamiids, which has not been satisfactorily divided into orders. Cynomorium was raised to familial status as Cynomoriaceae, and along with Apodanthaceae and Gumillea, remained unplaced in APG III. Five taxa were unplaced among the angiosperms in APG III because Nicobariodendron and Petenaea
were added to the list.
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
. This was confirmed in a study of wood
anatomy
in 2008. Before 2001, Leptaulus and the rest of Cardiopteridaceae had usually been placed in a broadly circumscribed
Icacinaceae
, which turned out to be polyphyletic.
Some botanists do not recognize Cardiopteridaceae as a family of six genera. Instead, they segregate
Cardiopteris into a monogeneric Cardiopteridaceae sensu stricto and place the other five genera in the family Leptaulaceae. The monophyly
of Leptaulaceae has never been tested with molecular data.
n tree Pottingeria might belong in the order Celastrales
. 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 unresolved pentatomy
consisting of Parnassiaceae
, Pottingeria
, Mortonia
, the pair (Quetzalia + Zinowiewia
), and the other genera of Celastraceae
. 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.
to southern China
, Burma, and northern India
. 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
.
, 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 strong statistical support
.
In their outgroup, they included four genera from Saxifragales
. These were Daphniphyllum
, Medusandra, Soyauxia
, and Peridiscus. In their phylogeny, Medusandra and Soyauxia formed a strongly supported clade
with Peridiscus, a member of the family Peridiscaceae
, the most basal
clade in Saxifragales. Wurdack and Davis recommended that Medusandra and Soyauxia both be transferred to Peridiscaceae. Thus the monogeneric family Medusandraceae is subsumed into Peridiscaceae. Soyauxia had been found to be close to Peridiscus in another study two years before. Wurdack and Davis also found that the family Rafflesiaceae and the genera Aneulophus, Centroplacus
, and Trichostephanus belong in the order Malpighiales.
s from tropical West Africa
. Wurdack and Davis found the traditional placement of Aneulophus in Erythroxylaceae
to be correct. Its position within the family remains uncertain.
Erythroxylaceae is a family of four genera. Erythroxylum
has about 230 species. Nectaropetalum has eight species and Pinacopodium has two. No one has yet produced a molecular phylogeny of the family.
, a genus that had only recently been removed from Celastrales. Bhesa was grouped with Centroplacus to become the second genus in Centroplacaceae. Bhesa consists of five species of trees from India
and Malesia
.
, but it was found to be deeply embedded in Samydaceae
. Many taxonomists
do not recognize Samydaceae as a separate family from Salicaceae
.
, Rhizanthes, and Rafflesia
. All of these are holoparasites
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 within Euphorbiaceae
sensu stricto, a circumscription of Euphorbiaceae that excludes Phyllanthaceae
, Picrodendraceae
, Putranjivaceae
, Pandaceae
, and a few other very small groups that had been included in it until the 1990s. In order to preserve Rafflesiaceae, Wurdack and Davis split Euphorbiaceae sensu stricto into Euphorbiaceae sensu strictissimo and Peraceae, a new family comprising Pera
and four other genera.
holoparasites
. In these, the chloroplast
gene
s that are usually used in phylogenetic studies of angiosperms have become nonfunctional pseudogene
s. If these evolve rapidly
, they may be saturated with repeated mutation
s at the same site and consequently not be useful for phylogenetic reconstruction.
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
.
. On the basis of mitochondrial DNA, Cytinaceae has been placed in Malvales
, as sister to Muntingiaceae
.
, but this result had only 76% maximum likelihood
bootstrap
support.
n trees, notable for their large leaves, up to 55cm long and 25 cm wide. It is usually placed by itself in the family Hoplestigmataceae which is thought to be related to Boraginaceae
. It has been suggested that Hoplestigma be placed within Boraginaceae.
Most of the phylogeny papers on Boraginaceae have been published obscurely and cover only tribes
or subfamilies
. No phylogeny of the family has been published in any of the widely available journals of botany.
and northwestern South America
. Ever since Hermann Karsten
proposed the name Metteniusaceae in 1859, some authors have placed Metteniusa by itself, in that family. Most authors, however, placed it in Icacinaceae
until that family was shown to be polyphyletic in 2001.
In 2007, in a comparison of DNA sequences for three genes, it was found that Metteniusa is one of the basal
clades of the lamiids. The authors recommended that the family Metteniusaceae be recognized. Nothing is yet known about relationships among the groups of basal lamiids. The groups
in this polytomy
include the order Garryales
, the families Icacinaceae
, Oncothecaceae, and Metteniusaceae, as well as some unplaced genera, including Apodytes
, Emmotum
, and Cassinopsis.
No phylogenetic study has focused on the lamiids, but phylogenies have been inferred for the asterids
, a group composed of Cornales
, Ericales
, the lamiids, and the campanulids.
, but its position within that order has not been determined.
Two researchers in Taiwan
announced on the internet in 2009 that they have results supporting the placement of Balanophoraceae in Santalales. They have yet to publish anything in a scientific journal
.
. It is not closely related to anything else, so it is placed in the monogeneric family Cynomoriaceae.
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. One study placed it in Saxifragales, but not at any particular position within that order. Doubts have been expressed about the results of this study. Another study placed Cynomorium in Rosales
based on analysis of the two invert repeat
regions of the chloroplast genome
, which evolve at one fifth the rate
of the two single copy regions.
which was collected in the late 18th century in Peru
. It was named by Hipólito Ruiz López
and José Antonio Pavón Jiménez
.
George Bentham
and Joseph Hooker
placed it in Cunoniaceae
, and this treatment was followed by Adolf Engler
and most others. The last comprehensive treatment of Cunoniaceae, however, excludes it from the family. In 2009, Armen Takhtajan
placed Gumillea in Simaroubaceae
. 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.
Gumillea has also been called a synonym
of Picramnia
, but the ultimate source of this information is obscure and it is not mentioned in either of the recent treatments of Picramnia. It is worth noting that on their plate
for Gumillea, Ruiz and Pavón showed 11 ovule
s or immature seed
s that had been extracted from a 2-locular
ovary
. But the ovary in Picramnia has (sometimes 2), usually 3 to 4 locules and there are always two ovules in each locule.
It might be possible to determine the affinities of Gumillea if DNA could be extracted from the existing specimen. DNA has been successfully amplified
from specimens of similar age. Any material used in such research, however, might never be replaced.
herbs
. These are distributed into three genera: Pilostyles
, Apodanthes, and Berlinianche. Attempts to determine the relationships of Apodanthaceae have produced only uncertain results and they remain as enigmatic as ever.
APG II system
The APG II system of plant classification is the second, now obsolete, version of a modern, mostly molecular-based, system of plant taxonomy that was published in April 2003 by the Angiosperm Phylogeny Group. It was a revision of the first APG system, published in 1998, and was superseded in 2009...
of plant classification
History of plant systematics
The history of plant systematics—the biological classification of plants—stretches from the work of ancient Greek to modern evolutionary biologists. As a field of science, plant systematics came into being only slowly, early plant lore usually being treated as part of the study of...
was published in April 2003, fifteen genera
Genera
Genera is a commercial operating system and development environment for Lisp machines developed by Symbolics. It is essentially a fork of an earlier operating system originating on the MIT AI Lab's Lisp machines which Symbolics had used in common with LMI and Texas Instruments...
and three families
Family (biology)
In biological classification, family is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order, genus, and species, with family fitting between order and genus. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the...
were placed incertae sedis
Incertae sedis
, is a term used to define a taxonomic group where its broader relationships are unknown or undefined. Uncertainty at specific taxonomic levels is attributed by , , and similar terms.-Examples:*The fossil plant Paradinandra suecica could not be assigned to any...
in the angiosperms, and were listed in a section of the appendix entitled "Taxa of uncertain position".
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By the end of 2009, molecular phylogenetic analysis of DNA sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
s had revealed the relationships
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
of most of these taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
, and all but three of them had been placed in some group
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
within the angiosperms. In October 2009, APG II was superseded by the APG III system
APG III system
The APG III system of flowering plant classification is the third version of a modern, mostly molecular-based, system of plant taxonomy...
. 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 the order
Order (biology)
In scientific classification used in biology, the order is# a taxonomic rank used in the classification of organisms. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and family...
Malpighiales
Malpighiales
Malpighiales is one of the largest orders of flowering plants, containing about 16000 species, approximately 7.8% of the eudicots. The order is very diverse and hard to recognize except with molecular phylogenetic evidence. It is not part of any of the classification systems that are based only on...
, close to Euphorbiaceae
Euphorbiaceae
Euphorbiaceae, the Spurge family are a large family of flowering plants with 300 genera and around 7,500 species. Most are herbs, but some, especially in the tropics, are also shrubs or trees. Some are succulent and resemble cacti....
and possibly within it. Mitrastema became a monotypic family, Mitrastemonaceae. This family and Balanophoraceae were placed incertae sedis into orders, that is, their positions within these orders remained completely unknown. Metteniusa was found to belong to a supraordinal
Taxonomic rank
In biological classification, rank is the level in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class. Each rank subsumes under it a number of less general categories...
group known as the lamiids, which has not been satisfactorily divided into orders. Cynomorium was raised to familial status as Cynomoriaceae, and along with Apodanthaceae and Gumillea, remained unplaced in APG III. Five taxa were unplaced among the angiosperms in APG III because Nicobariodendron and Petenaea
Petenaea
Petenaea cordata was first described in Elaeocarpaceae and later placed in Tiliaceae, but most authors have been uncertain about its familial affinities. It was considered a taxon incertae sedis in the Angiosperm Phylogeny Group classification...
were added to the list.
Leptaulus
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 studyResearch
Research can be defined as the scientific search for knowledge, or as any systematic investigation, to establish novel facts, solve new or existing problems, prove new ideas, or develop new theories, usually using a scientific method...
based on morphological
Plant morphology
Plant morphology or phytomorphology is the study of the physical form and external structure of plants. This is usually considered distinct from plant anatomy, which is the study of the internal structure of plants, especially at the microscopic level...
and DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
data, Leptaulus was found to belong to a group of six genera that most authors now consider to be the family Cardiopteridaceae
Cardiopteridaceae
Cardiopteridaceae is a eudicot family of flowering plants. It consists of about 43 species of trees, shrubs, and woody vines, mostly of the tropics, but with a few in temperate regions. It contains six genera, the largest of which is Citronella, with 21 species. The other genera are much smaller...
. This was confirmed in a study of wood
Wood
Wood is a hard, fibrous tissue found in many trees. It has been used for hundreds of thousands of years for both fuel and as a construction material. It is an organic material, a natural composite of cellulose fibers embedded in a matrix of lignin which resists compression...
anatomy
Plant anatomy
Plant anatomy or phytotomy is the general term for the study of the internal structure of plants. While originally it included plant morphology, which is the description of the physical form and external structure of plants, since the mid-20th century the investigations of plant anatomy are...
in 2008. Before 2001, Leptaulus and the rest of Cardiopteridaceae had usually been placed in a broadly circumscribed
Circumscription (taxonomy)
In taxonomy, circumscription is the definition of the limits of a taxonomic group of organisms. One goal of taxonomy is to achieve a stable circumscription for every taxonomic group. Achieving stability can be simple or difficult....
Icacinaceae
Icacinaceae
Icacinaceae is a family of flowering plants.It consists of trees, shrubs, and lianas, primarily of the tropics.The family was traditionally circumscribed quite broadly, with around 55 genera totalling over 400 species...
, which turned out to be polyphyletic.
Some botanists do not recognize Cardiopteridaceae as a family of six genera. Instead, they segregate
Segregate (taxonomy)
In taxonomy, a segregate, or a segregate taxon is created when a taxon is split off, from another taxon. This other taxon will be better known, usually bigger, and will continue to exist, even after the segregate taxon has been split off...
Cardiopteris into a monogeneric Cardiopteridaceae sensu stricto and place the other five genera in the family Leptaulaceae. The monophyly
Monophyly
In common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of the members of the group. The term is synonymous with the uncommon term holophyly...
of Leptaulaceae has never been tested with molecular data.
Pottingeria
It had long been thought, at least by some, that the small Southeast AsiaSoutheast Asia
Southeast Asia, South-East Asia, South East Asia or Southeastern Asia is a subregion of Asia, consisting of the countries that are geographically south of China, east of India, west of New Guinea and north of Australia. The region lies on the intersection of geological plates, with heavy seismic...
n tree Pottingeria might belong in the order Celastrales
Celastrales
Celastrales is an order of flowering plants. They are found throughout the tropics and subtropics, with only a few species extending far into the temperate regions. There are about 1200 to 1350 species in about 100 genera. All but 7 of these genera are in the large family Celastraceae...
. 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 unresolved pentatomy
Polytomy
A polytomy , meaning many temporal based branches, is a section of a phylogeny in which the evolutionary relationships can not be fully resolved to dichotomies. In a phylogenetic tree, a polytomy is represented as a node which has more than two immediate descending branches...
consisting of Parnassiaceae
Parnassiaceae
Parnassiaceae Gray is a family of Flowering plants in the eudicot order Celastrales. It is not recognized in the APG III system of plant classification. When that system was published in 2009, Parnassiaceae was treated as a segregate of an expanded Celastraceae. Parnassiaceae has only two...
, Pottingeria
Pottingeria
Pottingeria is a small tree or large shrub native to mountainous areas of southeast Asia .It had long been thought, at least by some, to belong in the order Celastrales. 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...
, Mortonia
Mortonia
Mortonia is a small genus of flowering shrubs known as saddlebushes or mortonias. These are rough, hairy shrubs with leathery leaves and panicles of fleshy white to purplish flowers. They bear nutlets containing 1 seed each...
, the pair (Quetzalia + Zinowiewia
Zinowiewia
Zinowiewia is a genus of plants in the family Celastraceae.Species include:* Z. costaricensis Lundell* Z. madsenii C. Ulloa & P. Jørg.* Z. micrantha Lundell...
), and the other genera of Celastraceae
Celastraceae
The Celastraceae , is a family of about 90-100 genera and 1,300 species of vines, shrubs and small trees, belonging to the order Celastrales...
. 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.
Dipentodon
Dipentodon has one species Dipentodon sinicus. It is nativeIndigenous (ecology)
In biogeography, a species is defined as native to a given region or ecosystem if its presence in that region is the result of only natural processes, with no human intervention. Every natural organism has its own natural range of distribution in which it is regarded as native...
to southern China
China
Chinese civilization may refer to:* China for more general discussion of the country.* Chinese culture* Greater China, the transnational community of ethnic Chinese.* History of China* Sinosphere, the area historically affected by Chinese culture...
, Burma, and northern India
India
India , officially the Republic of India , is a country in South Asia. It is the seventh-largest country by geographical area, the second-most populous country with over 1.2 billion people, and the most populous democracy in the world...
. In 2009, in a molecular phylogenetic study of the order Huerteales
Huerteales
Huerteales is the botanical name for an order of flowering plants. It is one of the 17 orders that make up the large eudicot group known as the rosids in the APG III system of plant classification. Within the rosids, it is one of the orders in Malvidae, a group formerly known as eurosids II and...
, it was shown that Dipentodon and Perrottetia
Perrottetia
Perrottetia is a genus of flowering plants in the family Dipentodontaceae. The fifteen species it contains occur in Asia from China to Australia, and in the Americas from Mexico to Peru.-Selected species:* Perrottetia excelsa Lund....
belong together as the two genera of the family Dipentodontaceae
Dipentodontaceae
Dipentodon is a genus of flowering plants in the family Dipentodontaceae. Its only species, Dipentodon sinicus, is a small, deciduous tree native to southern China, Burma, and northern India. It has been little studied and until recently its affinities remained obscure.- Description :Dipentodon...
.
Medusandra and Soyauxia
In 2009, in a molecular phylogenetic study of MalpighialesMalpighiales
Malpighiales is one of the largest orders of flowering plants, containing about 16000 species, approximately 7.8% of the eudicots. The order is very diverse and hard to recognize except with molecular phylogenetic evidence. It is not part of any of the classification systems that are based only on...
, 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 strong statistical support
Resampling (statistics)
In statistics, resampling is any of a variety of methods for doing one of the following:# Estimating the precision of sample statistics by using subsets of available data or drawing randomly with replacement from a set of data points # Exchanging labels on data points when performing significance...
.
In their outgroup, they included four genera from Saxifragales
Saxifragales
Saxifragales is an order of flowering plants. Their closest relatives are a large eudicot group known as the rosids by the definition of rosids given in the APG II classification system. Some authors define the rosids more widely, including Saxifragales as their most basal group. Saxifragales is...
. These were Daphniphyllum
Daphniphyllum
Daphniphyllum is a genus of flowering plants in the family Daphniphyllaceae, including about 25 species, all evergreen shrubs and trees native to east and southeast Asia...
, Medusandra, Soyauxia
Soyauxia
Soyauxia is a genus of flowering plants in the family Peridiscaceae. They are small trees or erect shrubs from wet forests of tropical West Africa. Eight specific names have been published in Soyauxia. Additional species have been discovered, but their names and descriptions will not be published...
, and Peridiscus. In their phylogeny, Medusandra and Soyauxia formed a strongly supported clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
with Peridiscus, a member of the family Peridiscaceae
Peridiscaceae
Peridiscaceae is a family of flowering plants in the order Saxifragales. It comprises four genera: Medusandra, Soyauxia, Peridiscus, and Whittonia. It has a disjunct distribution, with Peridiscus occurring in Venezuela and northern Brazil, Whittonia in Guyana, Medusandra in Cameroon, and Soyauxia...
, the most basal
Basal (phylogenetics)
In phylogenetics, a basal clade is the earliest clade to branch in a larger clade; it appears at the base of a cladogram.A basal group forms an outgroup to the rest of the clade, such as in the following example:...
clade in Saxifragales. Wurdack and Davis recommended that Medusandra and Soyauxia both be transferred to Peridiscaceae. Thus the monogeneric family Medusandraceae is subsumed into Peridiscaceae. Soyauxia had been found to be close to Peridiscus in another study two years before. Wurdack and Davis also found that the family Rafflesiaceae and the genera Aneulophus, Centroplacus
Centroplacus
Centroplacus is a genus of the family Centroplacaceae. It was formerly classified in the Phyllanthaceae and given its own tribe, the Centroplaceae....
, and Trichostephanus belong in the order Malpighiales.
Aneulophus
Aneulophus consists of two species of woody plantWoody plant
A woody plant is a plant that uses wood as its structural tissue. These are typically perennial plants whose stems and larger roots are reinforced with wood produced adjacent to the vascular tissues. The main stem, larger branches, and roots of these plants are usually covered by a layer of...
s from tropical West Africa
West Africa
West Africa or Western Africa is the westernmost region of the African continent. Geopolitically, the UN definition of Western Africa includes the following 16 countries and an area of approximately 5 million square km:-Flags of West Africa:...
. Wurdack and Davis found the traditional placement of Aneulophus in Erythroxylaceae
Erythroxylaceae
The Erythroxylaceae is a family of flowering plants consisting of 4 genera and approximately 240 species. The best-known species is the coca plant , the source of the drug cocaine....
to be correct. Its position within the family remains uncertain.
Erythroxylaceae is a family of four genera. Erythroxylum
Erythroxylum
Erythroxylum is a genus of tropical flowering plants in the family Erythroxylaceae. Many species contain the drug cocaine; Erythroxylum coca, a native of South America, is the main commercial source of cocaine and of the mild stimulant coca tea...
has about 230 species. Nectaropetalum has eight species and Pinacopodium has two. No one has yet produced a molecular phylogeny of the family.
Centroplacus
Centroplacus has a single species, Centroplacus glaucinus, a tree from West Africa. It was found to be close to BhesaBhesa
Bhesa is a genus of plant in family Centroplacaceae. A 2009 molecular phylogeny study places it in the family Centroplacaceae in the order Malpighiales.Species include:* Bhesa ceylanica, Ding Hou* Bhesa nitidissima, Kosterm....
, a genus that had only recently been removed from Celastrales. Bhesa was grouped with Centroplacus to become the second genus in Centroplacaceae. Bhesa consists of five species of trees from India
India
India , officially the Republic of India , is a country in South Asia. It is the seventh-largest country by geographical area, the second-most populous country with over 1.2 billion people, and the most populous democracy in the world...
and Malesia
Malesia
Malesia is a biogeographical region straddling the boundaries of the Indomalaya ecozone and Australasia ecozone, and also a phytogeographical floristic region in the Paleotropical Kingdom.-Floristic province:...
.
Trichostephanus
Trichostephanus has two species, both in tropical West Africa. It had usually been assigned to AchariaceaeAchariaceae
Achariaceae is a family of flowering plants, formerly consisting of 6 species in 3 genera of herb and shrubs endemic to southern Africa. More recently, the APG II system has greatly expanded the scope of the family by including many genera previously classified in the Flacourtiaceae. Molecular...
, but it was found to be deeply embedded in Samydaceae
Samydaceae
Samydaceae is a family of tropical and subtropical woody plants, its best known genus being Casearia. It has always been of uncertain placement, in the past usually being submerged in the family Flacourtiaceae....
. Many taxonomists
Taxonomy
Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
do not recognize Samydaceae as a separate family from Salicaceae
Salicaceae
Salicaceae are a family of flowering plants. Recent genetic studies summarized by the Angiosperm Phylogeny Group has greatly expanded the circumscription of the family to contain 55 genera....
.
Rafflesiaceae
Several genera have been removed from Rafflesiaceae, so that it now consists of only three genera: SapriaSapria
Sapria is a genus of parasitic flowering plants. It grows within roots of Vitis and Tetrastigma. The genus is limited to the tropical forests of South and South-east Asia....
, Rhizanthes, and Rafflesia
Rafflesia
Rafflesia is a genus of parasitic flowering plants. It contains approximately 28 species , all found in southeastern Asia, on the Malay Peninsula, Borneo, Sumatra, Thailand and the Philippines.Rafflesia was found in the Indonesian rain forest by an Indonesian guide working for Dr...
. All of these are holoparasites
Parasitic plant
A parasitic plant is one that derives some or all of its sustenance from another plant. About 4,100 species in approximately 19 families of flowering plants are known. Parasitic plants have a modified root, the haustorium, that penetrates the host plant and connects to the xylem, phloem, or...
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 within Euphorbiaceae
Euphorbiaceae
Euphorbiaceae, the Spurge family are a large family of flowering plants with 300 genera and around 7,500 species. Most are herbs, but some, especially in the tropics, are also shrubs or trees. Some are succulent and resemble cacti....
sensu stricto, a circumscription of Euphorbiaceae that excludes Phyllanthaceae
Phyllanthaceae
Phyllanthaceae is a family of flowering plants in the eudicot order Malpighiales. It is most closely related to the family Picrodendraceae. The Phyllanthaceae are most numerous in the tropics, with many in the south temperate zone, and a few ranging as far north as the middle of the north temperate...
, Picrodendraceae
Picrodendraceae
Picrodendraceae is a family of flowering plants, consisting of 80 species in 24 genera. These are subtropical to tropical and found in New Guinea, Australia, New Caledonia, Madagascar, continental Africa as well as tropical America....
, Putranjivaceae
Putranjivaceae
The rosid family Putranjivaceae is composed of about 210 species of evergreen tropical trees distributed into 4 genera. Members of this family have 2-ranked coriaceous leaves, which, if fresh, typically have a radish-like or peppery taste. The flowers are fasciculate and usually small, and the...
, Pandaceae
Pandaceae
The family Pandaceae consists of three genera that were formerly recognized in the Euphorbiaceae. Those are:*Galearia...
, and a few other very small groups that had been included in it until the 1990s. In order to preserve Rafflesiaceae, Wurdack and Davis split Euphorbiaceae sensu stricto into Euphorbiaceae sensu strictissimo and Peraceae, a new family comprising Pera
Pera (genus)
Pera is a genus of the flowering plant family Euphorbiaceae and the only genus of its tribe . Pera differs from other Euphorbiaceae in several characteristics and some classifications place it in its own family, Peraceae....
and four other genera.
Parasites
Four of the unplaced genera, and all three of the unplaced families of APG II consist of achlorophyllousChlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...
holoparasites
Parasitic plant
A parasitic plant is one that derives some or all of its sustenance from another plant. About 4,100 species in approximately 19 families of flowering plants are known. Parasitic plants have a modified root, the haustorium, that penetrates the host plant and connects to the xylem, phloem, or...
. In these, the chloroplast
Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...
gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s that are usually used in phylogenetic studies of angiosperms have become nonfunctional pseudogene
Pseudogene
Pseudogenes are dysfunctional relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell...
s. If these evolve rapidly
Mutation rate
In genetics, the mutation rate is the chance of a mutation occurring in an organism or gene in each generation...
, they may be saturated with repeated mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
s at the same site and consequently not be useful for phylogenetic reconstruction.
The relationships of some parasitic taxa have been elucidated in studies of nuclear
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
and mitochondrial DNA sequences. But these sequences sometimes produce artifactual
Artifact (error)
In natural science and signal processing, an artifact is any error in the perception or representation of any visual or aural information introduced by the involved equipment or technique....
topologies in the phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
, because horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
often occurs between parasites and their hosts
Host (biology)
In biology, a host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna...
.
Bdallophyton and Cytinus
The parasitic genera Bdallophyton and Cytinus have been found to be closely related and have been placed together as the family CytinaceaeCytinaceae
Cytinaceae is a family of parasitic flowering plant. It comprised two genera, Cytinus and Bdallophytum, totalling ten species.These two genera were formerly placed in family Rafflesiaceae, order Malpighiales. When they were first split out into a separate family, it was placed in Malpighiales, but...
. On the basis of mitochondrial DNA, Cytinaceae has been placed in Malvales
Malvales
Malvales are an order of flowering plants. As circumscribed by APG II-system, it includes about 6000 species within nine families. The order is placed in the eurosids II, which are part of the eudicots....
, as sister to Muntingiaceae
Muntingiaceae
Muntingiaceae is a family of flowering plants, belonging to the rosid order Malvales. It is a small family which consists of three monotypic genera: Dicraspidia, Muntingia and Neotessmannia. They are woody plants of the tropical regions of America. The older Cronquist System places these genera in...
.
Mitrastemon
The parasitic family Mitrastemonaceae has one genus, known either as Mitrastemon or Mitrastema. The genus name and the corresponding family name have been a source of much confusion. A phylogeny based on mitochondrial genes places Mitrastemon in the order EricalesEricales
The Ericales are a large and diverse order of dicotyledons, including for example tea, persimmon, blueberry, Brazil nut, and azalea. The order includes trees and bushes, lianas and herbaceous plants. Together with ordinary autophytic plants, the Ericales include chlorophyll-deficient...
, but this result had only 76% maximum likelihood
Maximum likelihood
In statistics, maximum-likelihood estimation is a method of estimating the parameters of a statistical model. When applied to a data set and given a statistical model, maximum-likelihood estimation provides estimates for the model's parameters....
bootstrap
Bootstrapping (statistics)
In statistics, bootstrapping is a computer-based method for assigning measures of accuracy to sample estimates . This technique allows estimation of the sample distribution of almost any statistic using only very simple methods...
support.
Hoplestigma
Hoplestigma consists of two species of AfricaAfrica
Africa is the world's second largest and second most populous continent, after Asia. At about 30.2 million km² including adjacent islands, it covers 6% of the Earth's total surface area and 20.4% of the total land area...
n trees, notable for their large leaves, up to 55cm long and 25 cm wide. It is usually placed by itself in the family Hoplestigmataceae which is thought to be related to Boraginaceae
Boraginaceae
Boraginaceae, the Borage or Forget-me-not family, include a variety of shrubs, trees, and herbs, totaling about 2,000 species in 146 genera found worldwide.A number of familiar plants belong to this family....
. It has been suggested that Hoplestigma be placed within Boraginaceae.
Most of the phylogeny papers on Boraginaceae have been published obscurely and cover only tribes
Tribe (biology)
In biology, a tribe is a taxonomic rank between family and genus. It is sometimes subdivided into subtribes.Some examples include the tribes: Canini, Acalypheae, Hominini, Bombini, and Antidesmeae.-See also:* Biological classification* Rank...
or subfamilies
Family (biology)
In biological classification, family is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order, genus, and species, with family fitting between order and genus. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the...
. No phylogeny of the family has been published in any of the widely available journals of botany.
Metteniusa
Metteniusa consists of seven species of trees in Central AmericaCentral America
Central America is the central geographic region of the Americas. It is the southernmost, isthmian portion of the North American continent, which connects with South America on the southeast. When considered part of the unified continental model, it is considered a subcontinent...
and northwestern South America
South America
South America is a continent situated in the Western Hemisphere, mostly in the Southern Hemisphere, with a relatively small portion in the Northern Hemisphere. The continent is also considered a subcontinent of the Americas. It is bordered on the west by the Pacific Ocean and on the north and east...
. Ever since Hermann Karsten
Gustav Karl Wilhelm Hermann Karsten
Gustav Karl Wilhelm Hermann Karsten was a German botanist and geologist. Born in Stralsund, he followed the example of Alexander von Humboldt and traveled 1844-56 to the north of South America. He died 1908 in Berlin-Grunewald....
proposed the name Metteniusaceae in 1859, some authors have placed Metteniusa by itself, in that family. Most authors, however, placed it in Icacinaceae
Icacinaceae
Icacinaceae is a family of flowering plants.It consists of trees, shrubs, and lianas, primarily of the tropics.The family was traditionally circumscribed quite broadly, with around 55 genera totalling over 400 species...
until that family was shown to be polyphyletic in 2001.
In 2007, in a comparison of DNA sequences for three genes, it was found that Metteniusa is one of the basal
Basal (phylogenetics)
In phylogenetics, a basal clade is the earliest clade to branch in a larger clade; it appears at the base of a cladogram.A basal group forms an outgroup to the rest of the clade, such as in the following example:...
clades of the lamiids. The authors recommended that the family Metteniusaceae be recognized. Nothing is yet known about relationships among the groups of basal lamiids. The groups
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
in this polytomy
Polytomy
A polytomy , meaning many temporal based branches, is a section of a phylogeny in which the evolutionary relationships can not be fully resolved to dichotomies. In a phylogenetic tree, a polytomy is represented as a node which has more than two immediate descending branches...
include the order Garryales
Garryales
The Garryales are a small order of dicotyledons, including only two families and three genera:* Family Garryaceae**Garrya**Aucuba* Family Eucommiaceae**Eucommia...
, the families Icacinaceae
Icacinaceae
Icacinaceae is a family of flowering plants.It consists of trees, shrubs, and lianas, primarily of the tropics.The family was traditionally circumscribed quite broadly, with around 55 genera totalling over 400 species...
, Oncothecaceae, and Metteniusaceae, as well as some unplaced genera, including Apodytes
Apodytes
Apodytes This genus consists of 3 species of evergreen trees, from tropical northeastern Australia, New Caledonia, Africa and Asia.-Description:...
, Emmotum
Emmotum
Emmotum is a genus of flowering plants. It belongs to an informal group of six genera known as the Emmotum group. These are: Calatola, Ottoschulzia, Oecopetalum, Poraqueiba, Emmotum, and Platea. Platea is native to Asia, while the others are from the New World...
, and Cassinopsis.
No phylogenetic study has focused on the lamiids, but phylogenies have been inferred for the asterids
Asterids
In the APG II system for the classification of flowering plants, the name asterids refers to a clade .Most of the taxa belonging to this clade had been referred to the Asteridae in the Cronquist system and to the Sympetalae in earlier systems...
, a group composed of Cornales
Cornales
Cornales is an order of flowering plants, basal among the asterids, containing about 600 species. Plants within Cornales usually have four-parted flowers, drupaceous fruits, and inferior gynoecia topped with disc-shaped nectaries...
, Ericales
Ericales
The Ericales are a large and diverse order of dicotyledons, including for example tea, persimmon, blueberry, Brazil nut, and azalea. The order includes trees and bushes, lianas and herbaceous plants. Together with ordinary autophytic plants, the Ericales include chlorophyll-deficient...
, the lamiids, and the campanulids.
Balanophoraceae
Balanophoraceae is a family of holoparasites with 44 species in 17 genera. For a long time, Cynomorium was usually included in this family, but it is now known to be unrelated. In 2005, Balanophoraceae was shown to be in the order SantalalesSantalales
Santalales is an order of flowering plants with a cosmopolitan distribution, but heavily concentrated in tropical and subtropical regions.Most have seeds without a testa, which is unusual for flowering plants...
, but its position within that order has not been determined.
Two researchers in Taiwan
Taiwan
Taiwan , also known, especially in the past, as Formosa , is the largest island of the same-named island group of East Asia in the western Pacific Ocean and located off the southeastern coast of mainland China. The island forms over 99% of the current territory of the Republic of China following...
announced on the internet in 2009 that they have results supporting the placement of Balanophoraceae in Santalales. They have yet to publish anything in a scientific journal
Scientific journal
In academic publishing, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research. There are thousands of scientific journals in publication, and many more have been published at various points in the past...
.
Cynomorium
Many names have been published in Cynomorium, but there are probably only two speciesCynomorium coccineum
Cynomorium coccineum is a parasitic perennial flowering plant in the Cynomoriaceae, a family consisting of only one species in the genus Cynomorium. Its wider relationships are uncertain...
. It is not closely related to anything else, so it is placed in the monogeneric family Cynomoriaceae.
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. One study placed it in Saxifragales, but not at any particular position within that order. Doubts have been expressed about the results of this study. Another study placed Cynomorium in Rosales
Rosales
Rosales is an order of flowering plants. It is one of the four orders in the nitrogen fixing clade of the fabids and is sister to a clade consisting of Fagales and Cucurbitales. It contains about 7700 species, distributed into about 260 genera. Rosales comprises nine families, the type family...
based on analysis of the two invert repeat
Inverted repeat
An inverted repeat is a sequence of nucleotides that is the reversed complement of another sequence further downstream.For example, 5'---GACTGC....GCAGTC---3'. When no nucleotides intervene between the sequence and its downstream complement, it is called a palindrome. Inverted repeats define the...
regions of the chloroplast genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, which evolve at one fifth the rate
Mutation rate
In genetics, the mutation rate is the chance of a mutation occurring in an organism or gene in each generation...
of the two single copy regions.
Gumillea
Gumillea has a single species, Gumillea auriculata, and is known from only one specimenSpecimen
A specimen is a portion/quantity of material for use in testing, examination, or study.BiologyA laboratory specimen is an individual animal, part of an animal, a plant, part of a plant, or a microorganism, used as a representative to study the properties of the whole population of that species or...
which was collected in the late 18th century in Peru
Peru
Peru , officially the Republic of Peru , is a country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean....
. It was named by Hipólito Ruiz López
Hipólito Ruiz López
Hipólito Ruiz López , or Hipólito Ruiz, was a Spanish botanist known for researching the floras of Peru and Chile during an expedition under Carlos III from 1777 to 1788...
and José Antonio Pavón Jiménez
José Antonio Pavón Jiménez
José Antonio Pavón Jiménez or José Antonio Pavón was a Spanish botanist known for researching the flora of Peru and Chile during an expedition under Carlos III from 1777 to 1788...
.
George Bentham
George Bentham
George Bentham CMG FRS was an English botanist, characterized by Duane Isely as "the premier systematic botanist of the nineteenth century".- Formative years :...
and Joseph Hooker
Joseph Dalton Hooker
Sir Joseph Dalton Hooker OM, GCSI, CB, MD, FRS was one of the greatest British botanists and explorers of the 19th century. Hooker was a founder of geographical botany, and Charles Darwin's closest friend...
placed it in Cunoniaceae
Cunoniaceae
The Cunoniaceae is a family of 26 genera and about 350 species of woody plants in the Antarctic flora, with many laurifolia species with glossy leaves endemic to laurel forest habitat. The family is native to Australia, New Caledonia, New Guinea, New Zealand, southern South America, the Mascarene...
, and this treatment was followed by Adolf Engler
Adolf Engler
Heinrich Gustav Adolf Engler was a German botanist. He is notable for his work on plant taxonomy and phytogeography, like Die Natürlichen Pflanzenfamilien , edited with Karl A. E...
and most others. The last comprehensive treatment of Cunoniaceae, however, excludes it from the family. In 2009, Armen Takhtajan
Armen Takhtajan
Armen Leonovich Takhtajan or Takhtajian , was a Soviet-Armenian botanist, one of the most important figures in 20th century plant evolution and systematics and biogeography. His other interests included morphology of flowering plants, paleobotany, and the flora of the Caucasus...
placed Gumillea in Simaroubaceae
Simaroubaceae
The Simaroubaceae is a small, mostly tropical, family in the order Sapindales. In recent decades it has been subject to much taxonomic debate, with several small families being split off...
. 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.
Gumillea has also been called a synonym
Synonym (taxonomy)
In scientific nomenclature, a synonym is a scientific name that is or was used for a taxon of organisms that also goes by a different scientific name. For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies...
of Picramnia
Picramnia
Picramnia is a genus of plant considered to be in the family Picramniaceae, but sometimes placed in Simaroubaceae. The name is conserved against the genera Pseudo-brasilium Adans., and Tariri Aubl., both which have been rejected .-Selected species:* P. acreana Ule* P. andrade-limae...
, but the ultimate source of this information is obscure and it is not mentioned in either of the recent treatments of Picramnia. It is worth noting that on their plate
Lithography
Lithography is a method for printing using a stone or a metal plate with a completely smooth surface...
for Gumillea, Ruiz and Pavón showed 11 ovule
Ovule
Ovule means "small egg". In seed plants, the ovule is the structure that gives rise to and contains the female reproductive cells. It consists of three parts: The integument forming its outer layer, the nucellus , and the megaspore-derived female gametophyte in its center...
s or immature seed
Seed
A seed is a small embryonic plant enclosed in a covering called the seed coat, usually with some stored food. It is the product of the ripened ovule of gymnosperm and angiosperm plants which occurs after fertilization and some growth within the mother plant...
s that had been extracted from a 2-locular
Locule
A locule is a small cavity or compartment within an organ or part of an organism ....
ovary
Ovary (plants)
In the flowering plants, an ovary is a part of the female reproductive organ of the flower or gynoecium. Specifically, it is the part of the pistil which holds the ovule and is located above or below or at the point of connection with the base of the petals and sepals...
. But the ovary in Picramnia has (sometimes 2), usually 3 to 4 locules and there are always two ovules in each locule.
It might be possible to determine the affinities of Gumillea if DNA could be extracted from the existing specimen. DNA has been successfully amplified
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
from specimens of similar age. Any material used in such research, however, might never be replaced.
Apodanthaceae
The family Apodanthaceae comprises 22 to 30 species of endoparasiticParasitism
Parasitism is a type of symbiotic relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host. Traditionally parasite referred to organisms with lifestages that needed more than one host . These are now called macroparasites...
herbs
Herbaceous plant
A herbaceous plant is a plant that has leaves and stems that die down at the end of the growing season to the soil level. They have no persistent woody stem above ground...
. These are distributed into three genera: Pilostyles
Pilostyles
Pilostyles is a genus of flowering plants placed in the family Apodanthaceae, or alternately, the Rafflesiaceae. It includes several species of parasitic plants that live inside the stems of other plants and produce tiny flowers that burst through the surface of the host plants' tissue...
, Apodanthes, and Berlinianche. Attempts to determine the relationships of Apodanthaceae have produced only uncertain results and they remain as enigmatic as ever.