![Identical cladograms](https://upload.wikimedia.org/wikipedia/commons/1/1b/Identical_cladograms.svg)
A cladogram (from
Greek
Greek may refer to:
Greece
Anything of, from, or related to Greece, a country in Southern Europe:
*Greeks, an ethnic group.
*Greek language, a branch of the Indo-European language family.
**Proto-Greek language, the assumed last common ancestor ...
''clados'' "branch" and ''gramma'' "character") is a diagram used in
cladistics
Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
to show relations among organisms. A cladogram is not, however, an
evolutionary tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
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 clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
, a group of organisms with a
last common ancestor
In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA) or concestor, of a set of organisms is the most recent individual from which all the organisms of the set are descended. The ...
. 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
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
sequencing data and
computational phylogenetics
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.
Generating a cladogram
Molecular versus morphological data
The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded,
notochord
In anatomy, the notochord is a flexible rod which is similar in structure to the stiffer cartilage. If a species has a notochord at any stage of its life cycle (along with 4 other features), it is, by definition, a chordate. The notochord consis ...
, 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
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
has become cheaper and easier,
molecular systematics
Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to ...
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
In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, ...
, 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 marker Retrotransposon markers are components of DNA which are used as cladistic markers. They assist in determining the common ancestry, or not, of related taxa. The "presence" of a given retrotransposon in related taxa suggests their orthologous integra ...
s, 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
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
was entirely random; this seems at least sometimes not to be the case, however.
Plesiomorphies and synapomorphies
Researchers must decide which character states are "ancestral" (''
plesiomorphies
In phylogenetics, a plesiomorphy ("near form") and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.
Plesiomorphy, symplesiomorphy, apomorphy, and ...
'') and which are derived (''
synapomorphies
In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
''), because only synapomorphic character states provide evidence of grouping. This determination 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.
Homoplasies
A
homoplasy
Homoplasy, in biology and phylogenetics, is the term used to describe a Phenotypic trait, feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from Homology (biology), homology, w ...
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 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
Phylogenetic signal is an evolutionary and ecological term, that describes the tendency or the pattern of related biological species to resemble each other more than any other species that is randomly picked from the same phylogenetic tree.
Chara ...
.
A well-known example of homoplasy due to convergent evolution would be the character, "presence of wings". Although the wings of birds,
bat
Bats are mammals of the order Chiroptera.''cheir'', "hand" and πτερόν''pteron'', "wing". With their forelimbs adapted as wings, they are the only mammals capable of true and sustained flight. Bats are more agile in flight than most bi ...
s, and insects serve the same function, each evolved independently, as can be seen by their
anatomy
Anatomy () is the branch of biology concerned with the study of the structure of organisms and their parts. Anatomy is a branch of natural science that deals with the structural organization of living things. It is an old science, having its ...
. 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, 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.
What is not a cladogram
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, 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.
Cladogram selection
There are several
algorithms
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing c ...
available to identify the "best" cladogram. Most algorithms use a
metric
Metric or metrical may refer to:
* Metric system, an internationally adopted decimal system of measurement
* An adjective indicating relation to measurement in general, or a noun describing a specific type of measurement
Mathematics
In mathema ...
to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of
optimization
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfi ...
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 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
The method of least squares is a standard approach in regression analysis to approximate the solution of overdetermined systems (sets of equations in which there are more equations than unknowns) by minimizing the sum of the squares of the res ...
,
neighbor-joining
In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually based on DNA or protein sequence data, the algorithm require ...
,
parsimony,
maximum likelihood
In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, ...
, and
Bayesian inference
Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, a ...
.
Biologists sometimes use 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, 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 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
Simulated annealing (SA) is a probabilistic technique for approximating the global optimum of a given function. Specifically, it is a metaheuristic to approximate global optimization in a large search space for an optimization problem. It ...
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
to branch within a larger clade.
Statistics
Incongruence length difference test (or partition homogeneity test)
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 is obtained for 100 replicates if 99 replicates have longer combined tree lengths.
Measuring homoplasy
Some measures attempt to measure the amount of homoplasy in a dataset with reference to a tree,
[reviewed in ] though it is not necessarily clear precisely what property these measures aim to quantify
Consistency index
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 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 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''/2in 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
, c
i occupies a range from 1 to
.
Retention index
The retention index (RI) 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 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.
Homoplasy Excess Ratio
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 a fully random dataset, and negative values indicate more homoplasy still (and tend only to occur in contrived examples). The HER is presented as the best measure of homoplasy currently available.
See also
* Phylogenetics
In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
* Dendrogram
* Basal (phylogenetics)
References
External links
*
{{Phylogenetics
Diagrams
Phylogenetics