A cladogram (from Greek clados "branch" and gramma "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade , a group of organisms with a last common ancestor . There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.
42-469: The rhyniophytes are a group of extinct early vascular plants that are considered to be similar to the genus Rhynia , found in the Early Devonian (around 419 to 393 million years ago ). Sources vary in the name and rank used for this group, some treating it as the class Rhyniopsida , others as the subdivision Rhyniophytina or the division Rhyniophyta . The first definition of
84-446: A t e s {\displaystyle n.states} , c i occupies a range from 1 to ( n . s t a t e s − 1 ) / ( n . t a x a − ⌈ n . t a x a / n . s t a t e s ⌉ ) {\displaystyle (n.states-1)/(n.taxa-\lceil n.taxa/n.states\rceil )} . The retention index (RI)
126-445: A metric to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization and minimization. In general, cladogram generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are modest (for example, just a few species and a couple of characteristics). Some algorithms are useful only when
168-540: A character in a phylogenetic analysis as they do not contribute anything to our understanding of relationships. However, homoplasy is often not evident from inspection of the character itself (as in DNA sequence, for example), and is then detected by its incongruence (unparsimonious distribution) on a most-parsimonious cladogram. Note that characters that are homoplastic may still contain phylogenetic signal . A well-known example of homoplasy due to convergent evolution would be
210-412: A cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded, notochord , unicellular, etc.) or molecular (DNA, RNA, or other genetic information). Prior to the advent of DNA sequencing, cladistic analysis primarily used morphological data. Behavioral data (for animals) may also be used. As DNA sequencing has become cheaper and easier, molecular systematics has become
252-422: A dataset, the degree to which each character carries phylogenetic information, and the fashion in which additive characters are coded, rendering it unfit for purpose. c i occupies a range from 1 to 1/[ n.taxa /2] in binary characters with an even state distribution; its minimum value is larger when states are not evenly spread. In general, for a binary or non-binary character with n . s t
294-457: A larger clade. The incongruence length difference test (ILD) is a measurement of how the combination of different datasets (e.g. morphological and molecular, plastid and nuclear genes) contributes to a longer tree. It is measured by first calculating the total tree length of each partition and summing them. Then replicates are made by making randomly assembled partitions consisting of the original partitions. The lengths are summed. A p value of 0.01
336-452: A more and more popular way to infer phylogenetic hypotheses. Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data. Approaches such as maximum likelihood , which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic retrotransposon markers , which are thought to be less prone to
378-631: A tree). The shape and symmetry of the sporangia was then used to divide up the group. Rhynialeans (order Rhyniales), such as Rhynia gwynne-vaughanii , Stockmansella and Huvenia , had radially symmetrical sporangia that were longer than wide and possessed vascular tissue with S-type tracheids. Cooksonioids, such as Cooksonia pertoni , C. paranensis and C. hemisphaerica , had radially symmetrical or trumpet-shaped sporangia, without clear evidence of vascular tissue. Renalioids, such as Aberlemnia , Cooksonia crassiparietilis and Renalia had bilaterally symmetrical sporangia and protosteles . There
420-604: A very early form of leaves. Vascular plant Vascular plants (from Latin vasculum 'duct'), also called tracheophytes ( UK : / ˈ t r æ k iː ə ˌ f aɪ t s / , US : / ˈ t r eɪ k iː ə ˌ f aɪ t s / ) or collectively tracheophyta ( / ˌ t r eɪ k iː ˈ ɒ f ɪ t ə / ; from Ancient Greek τραχεῖα ἀρτηρία ( trakheîa artēría ) 'windpipe' and φυτά ( phutá ) 'plants'), are plants that have lignified tissues (the xylem ) for conducting water and minerals throughout
462-410: Is a character state that is shared by two or more taxa due to some cause other than common ancestry. The two main types of homoplasy are convergence (evolution of the "same" character in at least two distinct lineages) and reversion (the return to an ancestral character state). Characters that are obviously homoplastic, such as white fur in different lineages of Arctic mammals, should not be included as
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#1732791809971504-566: Is an antiquated remnant of the obsolete scala naturae , and the term is generally considered to be unscientific. Botanists define vascular plants by three primary characteristics: Cavalier-Smith (1998) treated the Tracheophyta as a phylum or botanical division encompassing two of these characteristics defined by the Latin phrase "facies diploida xylem et phloem instructa" (diploid phase with xylem and phloem). One possible mechanism for
546-462: Is no agreement on the formal classification to be used for the rhyniophytes. The following are some of the names which may be used: In 2004, Crane et al. published a cladogram for the polysporangiophytes in which the Rhyniaceae are shown as the sister group of all other tracheophytes (vascular plants). Some other former "rhyniophytes", such as Horneophyton and Aglaophyton , are placed outside
588-411: Is obtained for 100 replicates if 99 replicates have longer combined tree lengths. Some measures attempt to measure the amount of homoplasy in a dataset with reference to a tree, though it is not necessarily clear precisely what property these measures aim to quantify The consistency index (CI) measures the consistency of a tree to a set of data – a measure of the minimum amount of homoplasy implied by
630-868: Is supported by several molecular studies. Other researchers state that taking fossils into account leads to different conclusions, for example that the ferns (Pteridophyta) are not monophyletic. Hao and Xue presented an alternative phylogeny in 2013 for pre- euphyllophyte plants. † Horneophytaceae [REDACTED] † Cooksoniaceae † Aglaophyton † Rhyniopsida [REDACTED] † Catenalis † Aberlemnia † Hsuaceae † Renaliaceae [REDACTED] † Adoketophyton †? Barinophytopsida † Zosterophyllopsida † Hicklingia † Gumuia † Nothia Lycopodiopsida [REDACTED] † Zosterophyllum deciduum † Yunia † Eophyllophyton † Trimerophytopsida † Ibyka † Pauthecophyton † Cladoxylopsida Polypodiopsida [REDACTED] Cladogram The characteristics used to create
672-526: Is usually done by comparison to the character states of one or more outgroups . States shared between the outgroup and some members of the in-group are symplesiomorphies; states that are present only in a subset of the in-group are synapomorphies. Note that character states unique to a single terminal (autapomorphies) do not provide evidence of grouping. The choice of an outgroup is a crucial step in cladistic analysis because different outgroups can produce trees with profoundly different topologies. A homoplasy
714-487: The Polysporangiophyte article for the expanded cladogram.) The taxon and informal terms corresponding to it have been used in different ways. Hao and Xue in 2013 circumscribed their Rhyniopsida quite broadly, dividing it into rhynialeans, cooksonioids and renalioids. Genera included by Hao and Xue are listed below, with assignments to their three subgroups where these are given. It has been suggested that
756-508: The "true" tracheophytes, the eutracheophytes. † Aglaophyton † Horneophytopsida † Rhyniophyta Lycopodiophyta † Zosterophyllophyta † Cladoxylopsida Equisetopsida (horsetails) Marattiopsida Psilotopsida (whisk ferns and adders'-tongues) Pteridopsida (true ferns) † Progymnospermophyta Cycadophyta (cycads) Ginkgophyta (ginkgo) Gnetophyta Pinophyta (conifers) Magnoliophyta (flowering plants) † Pteridospermatophyta (seed ferns) This phylogeny
798-549: The Rhynie chert Lagerstätte - rich fossil beds in Aberdeenshire , Scotland , and roughly coeval sites with similar flora. Used in this way, these terms refer to a floristic assemblage of more or less related early land plants, not a taxon . Though the rhyniophytes are well represented, plants with simpler anatomy , like Aglaophyton , are also common; there are also more complex plants, like Asteroxylon , which has
840-399: The ability to grow independent roots, woody structure for support, and more branching. A proposed phylogeny of the vascular plants after Kenrick and Crane 1997 is as follows, with modification to the gymnosperms from Christenhusz et al. (2011a), Pteridophyta from Smith et al. and lycophytes and ferns by Christenhusz et al. (2011b) The cladogram distinguishes the rhyniophytes from
882-431: The character, "presence of wings". Although the wings of birds, bats , and insects serve the same function, each evolved independently, as can be seen by their anatomy . If a bird, bat, and a winged insect were scored for the character, "presence of wings", a homoplasy would be introduced into the dataset, and this could potentially confound the analysis, possibly resulting in a false hypothesis of relationships. Of course,
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#1732791809971924-434: The characteristic data are molecular (DNA, RNA); other algorithms are useful only when the characteristic data are morphological. Other algorithms can be used when the characteristic data includes both molecular and morphological data. Algorithms for cladograms or other types of phylogenetic trees include least squares , neighbor-joining , parsimony , maximum likelihood , and Bayesian inference . Biologists sometimes use
966-691: The dataset). The rescaled consistency index (RC) is obtained by multiplying the CI by the RI; in effect this stretches the range of the CI such that its minimum theoretically attainable value is rescaled to 0, with its maximum remaining at 1. The homoplasy index (HI) is simply 1 − CI. This measures the amount of homoplasy observed on a tree relative to the maximum amount of homoplasy that could theoretically be present – 1 − (observed homoplasy excess) / (maximum homoplasy excess). A value of 1 indicates no homoplasy; 0 represents as much homoplasy as there would be in
1008-505: The group was found not to be monophyletic since some of its members are now known to lack vascular tissue. The definition that seems to be used most often now is that of D. Edwards and D.S. Edwards: "plants with smooth axes, lacking well-defined spines or leaves, showing a variety of branching patterns that may be isotomous, anisotomous, pseudomonopodial or adventitious. Elongate to globose sporangia were terminal on main axes or on lateral systems showing limited branching. It seems probable that
1050-662: The group, under the name Rhyniophytina, was by Banks , since when there have been many redefinitions, including by Banks himself. "As a result, the Rhyniophytina have slowly dissolved into a heterogeneous collection of plants ... the group contains only one species on which all authors agree: the type species Rhynia gwynne-vaughanii ". When defined very broadly, the group consists of plants with dichotomously branched, naked aerial axes ("stems") with terminal spore-bearing structures (sporangia). The rhyniophytes are considered to be stem group tracheophytes (vascular plants). The group
1092-705: The only reason a homoplasy is recognizable in the first place is because there are other characters that imply a pattern of relationships that reveal its homoplastic distribution. A cladogram is the diagrammatic result of an analysis, which groups taxa on the basis of synapomorphies alone. There are many other phylogenetic algorithms that treat data somewhat differently, and result in phylogenetic trees that look like cladograms but are not cladograms. For example, phenetic algorithms, such as UPGMA and Neighbor-Joining, group by overall similarity, and treat both synapomorphies and symplesiomorphies as evidence of grouping, The resulting diagrams are phenograms, not cladograms, Similarly,
1134-473: The plant. They also have a specialized non-lignified tissue (the phloem ) to conduct products of photosynthesis . The group includes most land plants ( c. 300,000 accepted known species) other than mosses . Vascular plants include the clubmosses , horsetails , ferns , gymnosperms (including conifers ), and angiosperms ( flowering plants ). They are contrasted with nonvascular plants such as mosses and green algae . Scientific names for
1176-421: The poorly preserved Eohostimella , found in deposits of Early Silurian age (Llandovery, around 440 to 430 million years ago ), may also be a rhyniophyte. Others have placed some of these genera in different groups. For example, Tortilicaulis has been considered to be a horneophyte . The general term " rhyniophytes " or " rhyniophytoids " is sometimes used for the assemblage of plants found in
1218-421: The presumed evolution from emphasis on haploid generation to emphasis on diploid generation is the greater efficiency in spore dispersal with more complex diploid structures. Elaboration of the spore stalk enabled the production of more spores and the development of the ability to release them higher and to broadcast them further. Such developments may include more photosynthetic area for the spore-bearing structure,
1260-499: The problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random; this seems at least sometimes not to be the case, however. Researchers must decide which character states are "ancestral" ( plesiomorphies ) and which are derived ( synapomorphies ), because only synapomorphic character states provide evidence of grouping. This determination
1302-436: The program settles on a local minimum rather than the desired global minimum. To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one. The basal position is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. A basal clade is the earliest clade (of a given taxonomic rank[a]) to branch within
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1344-405: The results of model-based methods (Maximum Likelihood or Bayesian approaches) that take into account both branching order and "branch length," count both synapomorphies and autapomorphies as evidence for or against grouping, The diagrams resulting from those sorts of analysis are not cladograms, either. There are several algorithms available to identify the "best" cladogram. Most algorithms use
1386-406: The subdivision, the group was treated as a division under the name Rhyniophyta. Taylor et al. in their book Paleobotany use Rhyniophyta as a formal taxon, but with a loose definition: plants "characterized by dichotomously branched, naked aerial axes with terminal sporangia". They thus include under "other rhyniophytes" plants apparently without vascular tissue. In 2010, the name paratracheophytes
1428-460: The term parsimony for a specific kind of cladogram generation algorithm and sometimes as an umbrella term for all phylogenetic algorithms. Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations,
1470-507: The tracheophyte clade, as they did not possess true vascular tissue (in particular did not have tracheids ). However, both Horneophyton and Aglaophyton have been tentatively classified as tracheophytes in at least one recent cladistic analysis of Early Devonian land plants. Partial cladogram by Crane et al. including the more certain rhyniophytes: Horneophytopsida Aglaophyton Huvenia Rhynia Stockmansella Lycopodiophytina and stem groups Euphyllophytina (See
1512-406: The tree. It is calculated by counting the minimum number of changes in a dataset and dividing it by the actual number of changes needed for the cladogram. A consistency index can also be calculated for an individual character i , denoted c i . Besides reflecting the amount of homoplasy, the metric also reflects the number of taxa in the dataset, (to a lesser extent) the number of characters in
1554-423: The user should input the data in various orders and compare the results. Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best". Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if
1596-463: The vascular plants group include Tracheophyta, Tracheobionta and Equisetopsida sensu lato . Some early land plants (the rhyniophytes ) had less developed vascular tissue; the term eutracheophyte has been used for all other vascular plants, including all living ones. Historically, vascular plants were known as " higher plants ", as it was believed that they were further evolved than other plants due to being more complex organisms. However, this
1638-419: The xylem, comprising a solid strand of tracheids, was centrarch." However, Edwards and Edwards also decided to include rhyniophytoids , plants which "look like rhyniophytes, but cannot be assigned unequivocally to that group because of inadequate anatomical preservation", but exclude plants like Aglaophyton and Horneophyton which definitely do not possess tracheids. In 1966, slightly before Banks created
1680-770: Was described as a subdivision of the division Tracheophyta by Harlan Parker Banks in 1968 under the name Rhyniophytina. The original definition was: "plants with naked (lacking emergences), dichotomizing axes bearing sporangia that are terminal, usually fusiform and may dehisce longitudinally; they are diminutive plants and, in so far as is known, have a small terete xylem strand with a central protoxylem." With this definition, they are polysporangiophytes , since their sporophytes consisted of branched stems bearing sporangia (spore-forming organs). They lacked leaves or true roots but did have simple vascular tissue . Informally, they are often called rhyniophytes or, as mentioned below, rhyniophytoids. However, as originally circumscribed ,
1722-399: Was proposed as an improvement of the CI "for certain applications" This metric also purports to measure of the amount of homoplasy, but also measures how well synapomorphies explain the tree. It is calculated taking the (maximum number of changes on a tree minus the number of changes on the tree), and dividing by the (maximum number of changes on the tree minus the minimum number of changes in
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1764-403: Was suggested, to distinguish such plants from 'true' tracheophytes or eutracheophytes. In 2013, Hao and Xue returned to the earlier definition. Their class Rhyniopsida (rhyniopsids) is defined by the presence of sporangia that terminate isotomous branching systems (i.e. the plants have branching patterns in which the branches are equally sized, rather than one branch dominating, like the trunk of
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