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Phylogenetic tree
A phylogenetic tree (also
phylogeny or evolutionary tree
[3]) is a branching diagram or a tree
showing the evolutionary
relationships among various
biological species or other entities
based upon similarities and
differences in their physical or
genetic characteristics. All life on
Earth is part of a single
phylogenetic tree, indicating
common ancestry.

In a rooted phylogenetic tree, each

node with descendants represents A phylogenetic tree based on rRNA genes, showing the three life domains:
bacteria, archaea, and eukaryota. The black branch at the bottom of the
the inferred most recent common
phylogenetic tree connects the three branches of living organisms to the
ancestor of those descendants, and
last universal common ancestor. In the absence of an outgroup, the root is
the edge lengths in some trees may
speculative.
be interpreted as time estimates.
Each node is called a taxonomic
unit. Internal nodes are generally
called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of
biology such as bioinformatics, systematics, and phylogenetics. Unrooted trees illustrate only the
relatedness of the leaf nodes and do not require the ancestral root to be known or inferred.

Contents
History
Properties
Rooted tree
Unrooted tree
Bifurcating versus multifurcating
Labeled versus unlabeled
Enumerating trees
Special tree types
Dendrogram
Cladogram
Phylogram
Dahlgrenogram
Phylogenetic network
Spindle diagram
Coral of life
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Construction
File formats
Limitations of phylogenetic analysis
See also
References
Further reading
External links
Images
General

History
The idea of a "tree of life" arose from
ancient notions of a ladder-like
progression from lower into higher
forms of life (such as in the Great
Chain of Being). Early
representations of "branching"
phylogenetic trees include a
"paleontological chart" showing the
geological relationships among A highly resolved, automatically generated tree of life, based on
plants and animals in the book completely sequenced genomes.[1][2]
Elementary Geology, by Edward
Hitchcock (first edition: 1840).

Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion of
an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary
biologists still use tree diagrams to depict evolution because such diagrams effectively convey the
concept that speciation occurs through the adaptive and semirandom splitting of lineages. Over time,
species classification has become less static and more dynamic.

The term phylogenetic, or phylogeny, derives from the two ancient greek words φῦλον (phûlon),
meaning "race, lineage", and γένεσις (génesis), meaning "origin, source".[4][5]

Properties

Rooted tree

A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node — the root —
corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of
the tree. The root node does not have a parent node, but serves as the parent of all other nodes in the
tree. The root is therefore a node of degree 2, while other internal nodes have a minimum degree of 3
(where "degree" here refers to the total number of incoming and outgoing edges).

The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to
allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.
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Unrooted tree

Unrooted trees illustrate the relatedness of the leaf nodes without

making assumptions about ancestry. They do not require the
ancestral root to be known or inferred.[7] Unrooted trees can always
be generated from rooted ones by simply omitting the root. By
contrast, inferring the root of an unrooted tree requires some means
Rooted phylogenetic tree optimized
of identifying ancestry. This is normally done by including an for blind people. The lowest point of
outgroup in the input data so that the root is necessarily between the the tree is the root, which
outgroup and the rest of the taxa in the tree, or by introducing symbolizes the universal common
additional assumptions about the relative rates of evolution on each ancestor to all living beings. The
branch, such as an application of the molecular clock hypothesis.[8] tree branches out into three main
groups: Bacteria (left branch, letters
a to i), Archea (middle branch,
Bifurcating versus multifurcating letters j to p) and Eukaryota (right
branch, letters q to z). Each letter
Both rooted and unrooted trees can be either bifurcating or corresponds to a group of
multifurcating. A rooted bifurcating tree has exactly two organisms, listed below this
descendants arising from each interior node (that is, it forms a description. These letters and the
binary tree), and an unrooted bifurcating tree takes the form of an description should be converted to
unrooted binary tree, a free tree with exactly three neighbors at each Braille font, and printed using a
internal node. In contrast, a rooted multifurcating tree may have Braille printer. The figure can be 3D
more than two children at some nodes and an unrooted printed by copying the png file and
multifurcating tree may have more than three neighbors at some using Cura or other software to
nodes. generate the Gcode for 3D printing.

Labeled versus unlabeled

Both rooted and unrooted trees can be either labeled or

unlabeled. A labeled tree has specific values assigned to its
leaves, while an unlabeled tree, sometimes called a tree
shape, defines a topology only. Some sequence-based trees
built from a small genomic locus, such as Phylotree,[9]
feature internal nodes labeled with inferred ancestral
haplotypes.

Enumerating trees An unrooted phylogenetic tree for myosin, a

superfamily of proteins.[6]
The number of possible trees for a given number of leaf
nodes depends on the specific type of tree, but there are
always more labeled than unlabeled trees, more multifurcating than bifurcating trees, and more rooted
than unrooted trees. The last distinction is the most biologically relevant; it arises because there are
many places on an unrooted tree to put the root. For bifurcating labeled trees, the total number of rooted
trees is:

for , represents the number of leaf nodes.[10]

For bifurcating labeled trees, the total number of unrooted trees is:[10]
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for .

Among labeled bifurcating trees, the number of unrooted trees with

leaves is equal to the number of rooted trees with leaves.[3]

The number of rooted trees grows quickly as a function of the

number of tips. For 10 tips, there are more than possible
bifurcating trees, and the number of multifurcating trees rises faster,
with ca. 7 times as many of the latter as of the former.

Counting trees.[10]
Increase in the total number of
All phylogenetic trees as a function of
Binary
Binary

Labeled
Multifurcating
possible

unrooted rooted the number of labeled leaves:

leaves rooted trees rooted
trees trees unrooted binary trees (blue
trees
diamonds), rooted binary trees (red
1 1 1 0 1 circles), and rooted multifurcating or
2 1 1 0 1 binary trees (green: triangles). The
Y-axis scale is logarithmic.
3 1 3 1 4
4 3 15 11 26
5 15 105 131 236
6 105 945 1,807 2,752
7 945 10,395 28,813 39,208
8 10,395 135,135 524,897 660,032
9 135,135 2,027,025 10,791,887 12,818,912
10 2,027,025 34,459,425 247,678,399 282,137,824

Special tree types

Dendrogram

A dendrogram is a general name for a tree, whether

phylogenetic or not, and hence also for the diagrammatic
representation of a phylogenetic tree.[11]

Cladogram Dendrogram of the phylogeny of some dog

breeds
A cladogram only represents a branching pattern; i.e., its
branch lengths do not represent time or relative amount of
character change, and its internal nodes do not represent ancestors.[12]

Phylogram

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A phylogram is a phylogenetic tree that has branch lengths

proportional to the amount of character change.[14]

A chronogram is a phylogenetic tree that explicitly

represents time through its branch lengths.[15]

Dahlgrenogram

A Dahlgrenogram is a diagram representing a cross section

of a phylogenetic tree

Phylogenetic network A chronogram of Lepidoptera.[13] In this

phylogenetic tree type, branch lengths are
proportional to geological time.
A phylogenetic network is not strictly speaking a tree, but
rather a more general graph, or a directed acyclic graph in
the case of rooted networks. They are used to overcome
some of the limitations inherent to trees.

Spindle diagram

A spindle diagram, or bubble diagram, is often called a

romerogram, after its popularisation by the American
palaeontologist Alfred Romer.[16]
It represents taxonomic
diversity (horizontal width) against geological time (vertical
axis) in order to reflect the variation of abundance of
various taxa through time.
However, a spindle diagram is
not an evolutionary tree:[17] the taxonomic spindles obscure
the actual relationships of the parent taxon to the daughter
taxon[16] and have the disadvantage of involving the
paraphyly of the parental group.[18]
This type of diagram is
no longer used in the form originally proposed.[18] A spindle diagram, showing the evolution of
the vertebrates at class level, width of spindles
indicating number of families. Spindle
Coral of life diagrams are often used in evolutionary
taxonomy.
Darwin[19] also mentioned that the coral may be a more
suitable metaphor than the tree. Indeed, phylogenetic corals
are useful for portraying past and present life, and they have some advantages over trees (anastomoses
allowed, etc.).[18]

Construction
Phylogenetic trees composed with a nontrivial number of input sequences are constructed using
computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA,
which calculate genetic distance from multiple sequence alignments, are simplest to implement, but do
not invoke an evolutionary model. Many sequence alignment methods such as ClustalW also create trees
by using the simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony
is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution
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(i.e. parsimony). More advanced methods use the optimality

criterion of maximum likelihood, often within a Bayesian
framework, and apply an explicit model of evolution to
phylogenetic tree estimation.[3] Identifying the optimal tree
using many of these techniques is NP-hard,[3] so heuristic
search and optimization methods are used in combination
with tree-scoring functions to identify a reasonably good
tree that fits the data.

Tree-building methods can be assessed on the basis of

several criteria:[20]

efficiency (how long does it take to compute the answer, The Coral of Life
how much memory does it need?)
power (does it make good use of the data, or is
information being wasted?)
consistency (will it converge on the same answer repeatedly, if each time given different data for the
same model problem?)
robustness (does it cope well with violations of the assumptions of the underlying model?)
falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)

Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using
T-theory.[21]

File formats

Trees can be encoded in a number of different formats, all of which must represent the nested structure
of a tree. They may or may not encode branch lengths and other features. Standardized formats are
critical for distributing and sharing trees without relying on graphics output that is hard to import into
existing software. Commonly used formats are

Nexus file format

Newick format

Limitations of phylogenetic analysis

Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different
species can provide evolutionary insight, these analyses have important limitations. Most importantly,
the trees that they generate are not necessarily correct – they do not necessarily accurately represent the
evolutionary history of the included taxa. As with any scientific result, they are subject to falsification by
further study (e.g., gathering of additional data, analyzing the existing data with improved methods).
The data on which they are based may be noisy;[22] the analysis can be confounded by genetic
recombination,[23] horizontal gene transfer,[24] hybridisation between species that were not nearest
neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences.

Also, there are problems in basing an analysis on a single type of character, such as a single gene or
protein or only on morphological analysis, because such trees constructed from another unrelated data
source often differ from the first, and therefore great care is needed in inferring phylogenetic
relationships among species. This is most true of genetic material that is subject to lateral gene transfer
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and recombination, where different haplotype blocks can have different histories. In these types of
analysis, the output tree of a phylogenetic analysis of a single gene is an estimate of the gene's phylogeny
(i.e. a gene tree) and not the phylogeny of the taxa (i.e. species tree) from which these characters were
sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies
generally use a combination of genes that come from different genomic sources (e.g., from mitochondrial
or plastid vs. nuclear genomes),[25] or genes that would be expected to evolve under different selective
regimes, so that homoplasy (false homology) would be unlikely to result from natural selection.

When extinct species are included as terminal nodes in an analysis (rather than, for example, to
constrain internal nodes), they are considered not to represent direct ancestors of any extant species.
Extinct species do not typically contain high-quality DNA.

The range of useful DNA materials has expanded with advances in extraction and sequencing
technologies. Development of technologies able to infer sequences from smaller fragments, or from
spatial patterns of DNA degradation products, would further expand the range of DNA considered
useful.

Phylogenetic trees can also be inferred from a range of other data types, including morphology, the
presence or absence of particular types of genes, insertion and deletion events – and any other
observation thought to contain an evolutionary signal.

Phylogenetic networks are used when bifurcating trees are not suitable, due to these complications
which suggest a more reticulate evolutionary history of the organisms sampled.

See also
Clade Generalized tree alignment
Cladistics List of phylogenetics software
Computational phylogenetics List of phylogenetic tree visualization software
Evolutionary biology Phylogenetic comparative methods
Evolutionary taxonomy

References
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22. Townsend JP, Su Z, Tekle Y (2012). "Phylogenetic Signal and Noise: Predicting the Power of a Data
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(https://pubmed.ncbi.nlm.nih.gov/31279710).

Further reading
Schuh, R. T. and A. V. Z. Brower. 2009. Biological Systematics: principles and applications (2nd
edn.) ISBN 978-0-8014-4799-0
Manuel Lima, The Book of Trees: Visualizing Branches of Knowledge, 2014, Princeton Architectural
Press, New York.
MEGA, a free software to draw phylogenetic trees.
Gontier, N. 2011. "Depicting the Tree of Life: the Philosophical and Historical Roots of Evolutionary
Tree Diagrams." Evolution, Education, Outreach 4: 515–538.

External links

Images
Human Y-Chromosome 2002 Phylogenetic Tree (https://web.archive.org/web/20120204215457/htt
p://ycc.biosci.arizona.edu/nomenclature_system/fig1.html)
iTOL: Interactive Tree Of Life (http://itol.embl.de/)
Phylogenetic Tree of Artificial Organisms Evolved on Computers (http://picbreeder.com/tol.php)

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Miyamoto and Goodman's Phylogram of Eutherian Mammals (https://web.archive.org/web/20110210

200039/http://phylogram.org/)

General
An overview of different methods of tree visualization is available at Page, R. D. M. (2011). "Space,
time, form: Viewing the Tree of Life". Trends in Ecology & Evolution. 27 (2): 113–120.
doi:10.1016/j.tree.2011.12.002 (https://doi.org/10.1016%2Fj.tree.2011.12.002). PMID 22209094 (http
s://pubmed.ncbi.nlm.nih.gov/22209094).
OneZoom: Tree of Life – all living species as intuitive and zoomable fractal explorer (responsive
design) (https://www.onezoom.org/life)
Discover Life (http://www.discoverlife.org/tree) An interactive tree based on the U.S. National
Science Foundation's Assembling the Tree of Life Project
PhyloCode (https://web.archive.org/web/20071114093618/http://www.ohiou.edu/phylocode/index.htm
l)
A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree (http://webarchive.loc.gov/a
ll/20011109204837/http://www.mrc-lmb.cam.ac.uk/myosin/trees/trees.html)
Tree of Life Web Project (http://tolweb.org/tree)
Phylogenetic inferring on the T-REX server (http://www.trex.uqam.ca)
NCBI's Taxonomy Database (https://www.ncbi.nlm.nih.gov/Taxonomy/)[1] (https://www.ncbi.nlm.nih.g
ov/Taxonomy/)
ETE: A Python Environment for Tree Exploration (https://web.archive.org/web/20140525220921/htt
p://ete.cgenomics.org/) This is a programming library to analyze, manipulate and visualize
phylogenetic trees. Ref. (http://www.biomedcentral.com/1471-2105/11/24)
A daily-updated tree of (sequenced) life (http://supfam.org/SUPERFAMILY/sTOL) Fang, H.; Oates,
M. E.; Pethica, R. B.; Greenwood, J. M.; Sardar, A. J.; Rackham, O. J. L.; Donoghue, P. C. J.;
Stamatakis, A.; De Lima Morais, D. A.; Gough, J. (2013). "A daily-updated tree of (sequenced) life as
a reference for genome research" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504836).
Scientific Reports. 3: 2015. Bibcode:2013NatSR...3E2015F (https://ui.adsabs.harvard.edu/abs/2013
NatSR...3E2015F). doi:10.1038/srep02015 (https://doi.org/10.1038%2Fsrep02015). PMC 6504836
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504836). PMID 23778980 (https://pubmed.ncbi.nlm.
nih.gov/23778980).

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