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.
43-619: A caiman ( / ˈ k eɪ m ə n / (also spelled cayman ) from Taíno kaiman ) is an alligatorid belonging to the subfamily Caimaninae , one of two primary lineages within the Alligatoridae family , the other being alligators . Caimans are native to Central and South America and inhabit marshes , swamps , lakes , and mangrove rivers. They have scaly skin and live a fairly nocturnal existence. They are relatively small-sized crocodilians with an average maximum weight of 6 to 40 kg (13 to 88 lb) depending on species, with
86-446: 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)
129-445: 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
172-537: 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
215-422: 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
258-431: A different vowel), and to-, tu- 'her'. Recorded conjugated verbs include daka ("I am"), waibá ("we go" or "let us go"), warikẽ ("we see"), kãma ("hear", imperative), ahiyakawo ("speak to us") and makabuka ("it is not important"). Verb-designating affixes were a-, ka-, -a, -ka, -nV in which "V" was an unknown or changeable vowel. This suggests that, like many other Arawakan languages, verbal conjugation for
301-445: A giant Miocene genus that grew to 12 m (39 ft) and the equally large Mourasuchus , which had a wide duck -like snout. Caimans are predators and, like alligators and crocodiles, their diet largely consists of fish. Caimans also hunt insects, birds, small mammals and reptiles. Due to their large size and ferocious nature, caimans have few natural predators within their environments. Humans are their main predators, because
344-418: A large nest in which to lay their eggs. The nests can be more than 1.5 m (4.9 ft) wide. Female caimans lay between 10 and 50 eggs, which hatch within about six weeks. Once they have hatched, the mother caiman takes her young to a shallow pool of water, where they can learn how to hunt and swim. The juveniles of spectacled caiman have been shown to stay together in pods for up to 18 months. Caimaninae
387-457: 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
430-540: A subject resembled the possessive prefixes on nouns. The negating prefix was ma- and the attributive prefix was ka- . Hence makabuka meant "it is not important". The buka element has been compared to the Kalinago suffix -bouca which designates the past tense. Hence, makabuka can be interpreted as meaning "it has no past". However, the word can also be compared to the Kalinago verb aboúcacha meaning "to scare". This verb
473-483: Is cladistically defined as Caiman crocodylus (the spectacled caiman ) and all species closer to it than to Alligator mississippiensis (the American alligator ). This is a stem-based definition for caimaninae, and means that it includes more basal extinct caimanine ancestors that are more closely related to living caimans than to alligators . The clade Jacarea includes the most derived caimans, being defined as
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#1733085763767516-410: 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
559-663: Is an Arawakan language formerly spoken widely by the Taíno people of the Caribbean . In its revived form, there exist several modern day Taíno language variants including Hiwatahia-Taino and Tainonaiki. At the time of Spanish contact , it was the most common language throughout the Caribbean. Classic Taíno (Taíno proper) was the native language of the Taíno tribes living in the Leeward Islands of
602-740: Is an alternative cladogram from Bona et al. 2018. Alligatorinae ( stem-based group ) Stangerochampsa † Albertochampsa † Brachychampsa † Protocaiman † Gnatusuchus † Globidentosuchus † Eocaiman † Notocaiman † Kuttanacaiman † Purussaurus † Mourasuchus † Necrosuchus † Tsoabichi † Paleosuchus trigonatus Smooth-fronted caiman Paleosuchus palpebrosus Cuvier's dwarf caiman Centenariosuchus † Caiman latirostris Broad-snouted caiman Melanosuchus niger Black caiman Caiman yacare Yacare caiman Caiman crocodilus Spectacled caiman Ta%C3%ADno language Taíno
645-411: 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
688-1147: Is shared in various Caribbean Arawakan languages such as Lokono ( bokaüya 'to scare, frighten') and Parauhano ( apüüta 'to scare'). In this case makabuka would mean "it does not frighten [me]". Modern day Taíno language variants follow slightly different grammar and word order from each other. Taíno borrowed words from Spanish, adapting them to its phonology. These include isúbara ("sword", from espada ), isíbuse ("mirror", from espejo ) and Dios ( God in Christianity , from Dios ). English words derived from Taíno include: barbecue , caiman , canoe , cassava , cay , guava , hammock , hurricane , hutia , iguana , macana , maize , manatee , mangrove , maroon , potato , savanna , and tobacco . Taíno loanwords in Spanish include: agutí , ají , auyama , batata , cacique , caoba , guanabana , guaraguao , jaiba , loro , maní , maguey (also rendered magüey ), múcaro , nigua , querequequé , tiburón , and tuna , as well as
731-586: Is the use of genomic retrotransposon markers , which are thought to be less prone to 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
774-526: 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
817-704: The Lesser Antilles , Boriken also known as Puerto Rico , the Turks and Caicos Islands , most of Ayiti-Kiskeya also known as Hispaniola , and eastern Cuba . The Ciboney dialect is essentially unattested, but colonial sources suggest it was very similar to Classic Taíno, and was spoken in the westernmost areas of Hispaniola, the Bahamas , Jamaica , and most of Cuba . By the late 15th century, Taíno had displaced earlier languages, except in western Cuba and pockets in Hispaniola. As
860-634: The diaspora . In 2023, activist Jorge Baracutay Estevez and the Higuayagua Taino cultural organization he chairs (as " kasike ") with help of linguist Alexandra Aikhenvald released Hiwatahia: Hekexi Taino Language Reconstruction , a formatted 20,000 word dictionary basing on languages of the wider Ta-Maipurean branch. Cladogram The characteristics used to create 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
903-474: The Caribbean are carrying out language revitalization efforts. Higuayagua published the "Hiwatahia-Taino Language Dictionary" and provide classes for their community. The Taíno language was not written. The Taínos used petroglyphs , but there has been little research in the area. The following phonemes are reconstructed from Spanish records: There was also a flap [ ɾ ] , which appears to have been an allophone of /d/ . The /d/ realization occurred at
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#1733085763767946-423: The Taíno culture declined during Spanish colonization, the language was replaced by Spanish and other European languages, such as English and French. Although the language declined drastically due to colonization, it continued to be spoken in isolated pockets in the Caribbean until the 19th century. As Spanish, English, and French became the dominant languages, some Taíno words were absorbed into those languages. As
989-587: 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 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
1032-466: The animals have been hunted for their meat and skin. Jaguars , anacondas and crocodiles are the only other predators of caimans, although they usually prey on the smaller specimens or specific species of caiman such as the Spectacled Caiman and Yacare caiman . During summer or droughts, caimans may dig a burrow and go into a form of summer hibernation called aestivation . Female caimans build
1075-489: The beginning of a word and the /ɾ/ realization occurred between vowels. Some Spanish writers used the letter ⟨x⟩ in their transcriptions, which could represent /h/ , /s/ or /ʃ/ in the Spanish orthography of their day. A distinction between /ɛ/ and /e/ is suggested by Spanish transcriptions of e vs ei/ey , as in ceiba "ceiba". The /e/ is written ei or final é in modern reconstructions. There
1118-431: 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,
1161-434: 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
1204-685: 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
1247-601: The exception of the black caiman ( Melanosuchus niger ), which can grow more than 4 m (13 ft) in length and weigh in excess of 450 kg (1,000 Ib). The black caiman is the largest caiman species in the world and is found in the slow-moving rivers and lakes that surround the Amazon basin. The smallest species is the Cuvier's dwarf caiman ( Paleosuchus palpebrosus ), which grows to 1.2 to 1.5 m (3.9 to 4.9 ft) long. There are six different species of caiman found throughout
1290-634: The first Indigenous language encountered by Europeans in the Americas, it was a major source of new words borrowed into European languages. Granberry & Vescelius (2004) distinguish two dialects, one on Hispaniola and further east, and the other on Hispaniola and further west. Columbus wrote that "...from Bahama to Cuba, Boriquen to Jamaica, the same language was spoken in various slight dialects, but understood by all." There are several modern day Taino language variants including: Hiwatahia-Taino and Tainonaiki. Modern day Taino tribes such as Higuayagua Taino of
1333-1010: The last common ancestor of Caiman latirostris (Broad-snouted caiman), Caiman crocodilus (Spectacled caiman), Caiman yacare (Yacare caiman), Melanosuchus niger (Black caiman), and all its descendants. Below is a cladogram showing the phylogeny of Caimaninae, modified from Hastings et al. (2013). † Stangerochampsa mccabei † Brachychampsa montana † Brachychampsa sealeyi Alligatorinae † Culebrasuchus mesoamericanus † Eocaiman cavernensis † Tsoabichi greenriverensis Paleosuchus palpebrosus Cuvier's dwarf caiman Paleosuchus trigonatus Smooth-fronted caiman † Centenariosuchus gilmorei † Purussaurus neivensis † Mourasuchus spp. † Orthogenysuchus olseni Caiman crocodilus Spectacled caiman Caiman yacare Yacare caiman Caiman latirostris Broad-snouted caiman † Caiman lutescens † Melanosuchus fisheri Melanosuchus niger Black caiman Here
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1376-585: The masculine gender, as in warokoel "our grandfather". Some words are recorded as ending in x , which may have represented a word-final /h/ sound. In general, stress was predictable and fell on the penultimate syllable of a word, unless the word ended in /e/ , /i/ or a nasal vowel, in which case it fell on the final syllable. Classic Taíno is not well attested. However, from what can be gathered, nouns appear to have had noun-class suffixes, as in other Arawakan languages. Attested Taíno possessive prefixes are da- 'my', wa- 'our', li- 'his' (sometimes with
1419-705: 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,
1462-426: The previous English words in their Spanish form: barbacoa , caimán , canoa, casabe , cayo, guayaba, hamaca, huracán, iguana, jutía, macana , maíz, manatí, manglar, cimarrón, patata, sabana, and tabaco . Place names of Taíno origin include: Six sentences of spoken Taíno were preserved. They are presented first in the original orthography in which they were recorded, then in a regularized orthography based on
1505-436: 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
1548-422: The reconstructed language and lastly in their English translation: Since the 2010s, there have been several publications that attempt at reconstructing modern Taíno lexicons by way of comparative linguistics with other related Arawak languages. Puertorican linguist Javier Hernandez published his Primario Basíco del Taíno-Borikenaíki in 2018 after a 16-year spanning research project with positive reception among
1591-405: 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
1634-460: 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,
1677-406: 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
1720-423: 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
1763-647: The watery jungle habitats of Central and Southern America. The average length for most of the other caiman species is about 2 to 2.5 m (6.6 to 8.2 ft) long. Caimans are distinguished from alligators, their closest relatives, by a few defining features: a lack of a bony septum between the nostrils, ventral armor composed of overlapping bony scutes formed from two parts united by a suture, and longer and sharper teeth than alligators, plus caimans tend to be more agile and crocodile-like in their movements. The calcium rivets on caiman scales make their hides stiffer. Several extinct forms are known, including Purussaurus ,
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1806-408: Was also a high back vowel [u] , which was often interchangeable with /o/ and may have been an allophone. There was a parallel set of nasal vowels . The nasal vowels /ĩ/ and /ũ/ were rare. Consonant clusters were not permitted in the onset of syllables. The only consonant permitted at the end of a syllable or word in most cases was /s/ . One exception was the suffix -(e)l , which indicated
1849-399: 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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