Phylogenetic tree

A phylogenetic tree or evolutionary

tree is a branching diagram or "tree"
showing the evolutionary relationships
among various biological species or
other entities—their phylogeny
(/faɪˈlɒdʒəni/)—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 the inferred
A speculatively rooted tree forrRNA genes, showing the three life domains:
most recent common ancestor of those
bacteria, archaea, and eukaryota. The black trunk at the bottom of the tree
descendants, and the edge lengths in
links the three branches of living organisms to thelast universal common
some trees may be interpreted as time ancestor.
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
Types
Rooted tree
Unrooted tree
Bifurcating tree
Special tree types
Construction
Limitations
A rooted phylogenetic tree, illustrating how Eukaryota and Archaea are more
See also closely related to each other than toBacteria (based on Cavalier-Smith's
References theory of bacterial evolution).Neomura is a clade composed of two life
domains, Archaea and Eukaryota.
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 plants and animals in the bookElementary 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 twoancient greek words φῦλον (phûlon), meaning "race, lineage", andγένεσις
(génesis), meaning "origin, source".[1][2]

Types

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.

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.[4]
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 of identifying ancestry.
This is normally done by including an outgroup in the input
data so that the root is necessarily between the outgroup and
the rest of the taxa in the tree, or by introducing additional
assumptions about the relative rates of evolution on each
branch, such as an application of the molecular clock
hypothesis.[5]
An unrooted phylogenetic tree formyosin, a superfamily
of proteins.[3]
Bifurcating tree
Both rooted and unrooted phylogenetic trees can be either
bifurcating or multifurcating, and either labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each
interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree
with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some
nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values
assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees
for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees,
more labeled than unlabeled 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 labeled bifurcating trees, there are:

total rooted trees and

total unrooted trees, where represents the number of leaf nodes. Among labeled bifurcating trees, the number of unrooted trees with
leaves is equal to the number of rooted trees with leaves.[6]

Special tree types

A dendrogram is a general name for a tree, whether phylogenetic or not,
and hence also for the diagrammatic representation of a phylogenetic
tree.[9]
A cladogram is a phylogenetic tree formed usingcladistic methods. This
type of tree only represents a branching pattern; i.e., its branch spans
do not represent time or relative amount of character change. [10]

A phylogram is a phylogenetic tree that has branch spans proportional

to the amount of character change.[11]
A chronogram is a phylogenetic tree that explicitly represents
evolutionary time through its branch spans. A spindle diagram, showing the
A spindle diagram (often called a Romerogram after the American evolution of the vertebrates at class
palaeontologist Alfred Romer) is the representation of the evolution and
level, width of spindles indicating
abundance of the various taxa through time.
number of families. Spindle diagrams
A Dahlgrenogram is a diagram representing a cross section of a
phylogenetic tree are often used in evolutionary
taxonomy.
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 thelimitations inherent to
trees.

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 (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.[6] Identifying the optimal tree using many of these techniques is NP-hard,[6] so heuristic
search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the
data.

[12]
Tree-building methods can be assessed on the basis of several criteria:

efficiency (how long does it take to compute he

t answer, 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 usingT-theory.[13]

Limitations
Although phylogenetic trees produced on the basis of
sequenced genes or genomic data in different species can
provide evolutionary insight, they have important limitations.
Most importantly, they do not necessarily accurately
represent the evolutionary history of the included taxa. In
fact, they are literally scientific hypotheses, 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 is noisy;[14] the analysis
A highly resolved, automatically generatedtree of life,
can be confounded by genetic recombination,[15] horizontal
based on completely sequenced genomes.[7][8]
gene transfer,[16] 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 the 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 and recombination, where different haplotype blocks can have different histories. In general, the output tree of a
phylogenetic analysis is an estimate of thecharacter'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), 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 in a tree, they are terminal nodes, as it is unlikely that they are direct ancestors of any extant
species. Skepticism might be applied when extinct species are included in trees that are wholly or partly based on DNA sequence
data, because little useful "ancient DNA" is preserved for longer than 100,000 years, and except in the most unusual circumstances no
DNA sequences long enough for use in phylogenetic analyses have yet been recovered from material over 1 million years old.

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.

In some organisms, endosymbionts have an independent genetic history from the host.

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

References
1. Bailly, Anatole (1981-01-01).Abrégé du dictionnaire grec français(https://www.worldcat.org/oclc/461974285). Paris:
Hachette. ISBN 978-2010035289. OCLC 461974285 (https://www.worldcat.org/oclc/461974285).
2. Bailly, Anatole. "Greek-french dictionary online"(http://www.tabularium.be/bailly/). www.tabularium.be. Archived (htt
p://archive.wikiwix.com/cache/20171203112515/http://www .tabularium.be/bailly/) from the original on December 3,
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3. Hodge T, Cope M (1 October 2000)."A myosin family tree" (http://jcs.biologists.org/cgi/content/full/113/19/3353)
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Cell Sci. 113 (19): 3353–4. PMID 10984423 (https://www.ncbi.nlm.nih.gov/pubmed/10984423). Archived (https://we
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The Scientist. 16: 18. Archived (https://web.archive.org/web/20031002231607/http://www .the-scientist.com/yr2002/s
ep/research1_020916.html)from the original on 2003-10-02.
6. Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
7. Letunic, Ivica; Bork, Peer (1 January 2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree
display and annotation"(http://itol.embl.de/help/17050570.pdf)(PDF). Bioinformatics. Cambridge. 23 (1): 127–128.
doi:10.1093/bioinformatics/btl529(https://doi.org/10.1093%2Fbioinformatics%2Fbtl529) . ISSN 1367-4803 (https://ww
w.worldcat.org/issn/1367-4803). PMID 17050570 (https://www.ncbi.nlm.nih.gov/pubmed/17050570). Archived (http
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8. Ciccarelli, FD; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006)."Toward automatic reconstruction of a
highly resolved tree of life"(http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf)(Submitted manuscript).
Science. 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C (http://adsabs.harvard.edu/abs/2006Sci...311.1283C) .
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9. Fox, Emily. "The dendrogram" (https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrog
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with Applications, Volume 78, 2017, Pages 32-50, ISSN 0957-4174,https://doi.org/10.1016/j.eswa.2017.02.012.
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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.

External links

Images
Human Y-Chromosome 2002 Phylogenetic Tree
iTOL: Interactive Tree Of Life
Phylogenetic Tree of Artificial Organisms Evolved on Computers
Miyamoto and Goodman's Phylogram of Eutherian Mammals

General
An overview of different methods of tree visualization is available atPage, 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.
Discover Life An interactive tree based on the U.S. National Science Foundation's Assembling theree T of Life
Project
PhyloCode
A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic ree T
Tree of Life Web Project
Phylogenetic inferring on the T-REX server
NCBI's Taxonomy Database[1]
ETE: A Python Environment for Tree Exploration This is a programming library to analyze, manipulate and visualize
phylogenetic trees. Ref.
A daily-updated tree of (sequenced) lifeFang, 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".Scientific Reports. 3: 2015.
Bibcode:2013NatSR...3E2015F. doi:10.1038/srep02015. PMID 23778980.

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