Phylogenetic tree

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A phylogenetic tree based on rRNA genes,[citation needed] showing the three life domains: bacteria, archaea,

and eukaryota. The black branch at the bottom of the phylogenetic tree connects the three branches of
living organisms to the last universal common ancestor. In the absence of an outgroup, the root is
speculative.

A highly resolved, automatically generated tree of life, based on completely sequenced genomes.[1][2]

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 the
inferred most recent common ancestor of those descendants, and the edge lengths
in some trees may 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

 1History
 2Properties
o 2.1Rooted tree
o 2.2Unrooted tree
o 2.3Bifurcating versus multifurcating
o 2.4Labeled versus unlabeled
o 2.5Enumerating trees
 3Special tree types
o 3.1Dendrogram
o 3.2Cladogram
o 3.3Phylogram
o 3.4Chronogram
o 3.5Dahlgrenogram
o 3.6Phylogenetic network
o 3.7Spindle diagram
o 3.8Coral of life
 4Construction
o 4.1File formats
 5Limitations of phylogenetic analysis
 6See also
 7References
 8Further reading
 9External links
o 9.1Images
o 9.2General

History[edit]
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
book 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[edit]
Rooted tree[edit]

Rooted phylogenetic tree optimized for blind people. The lowest point of the tree is the root, which
symbolizes the universal common ancestor to all living beings. The tree branches out into three main
groups: Bacteria (left branch, letters a to i), Archea (middle branch, letters j to p) and Eukaryota (right
branch, letters q to z). Each letter corresponds to a group of organisms, listed below this description. These
letters and the description should be converted to Braille font, and printed using a Braille printer. The figure
can be 3D printed by copying the png file and using Cura or other software to generate the Gcode for 3D
printing.

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[edit]
An unrooted phylogenetic tree for myosin, a superfamily of proteins.[6]

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 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.[8]
Bifurcating versus multifurcating[edit]
Both rooted and unrooted trees can be either bifurcating or multifurcating. 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.
Labeled versus unlabeled[edit]
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[edit]
Increase in the total number of phylogenetic trees as a function of the number of labeled leaves: unrooted
binary trees (blue diamonds), rooted binary trees (red circles), and rooted multifurcating or binary trees
(green: triangles). The Y-axis scale is logarithmic.

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]
 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]

Labele Multifurcatin
Binary Binary All possible
d g
unrooted trees rooted trees rooted trees
leaves rooted trees

1 1 1 0 1

2 1 1 0 1

3 1 3 1 4
 Counting trees.[10]

Labele Multifurcatin
Binary Binary All possible
d g
unrooted trees rooted trees rooted trees
leaves rooted trees

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[edit]

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Dendrogram[edit]

Dendrogram of the phylogeny of some dog breeds

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[edit]
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[edit]
A phylogram is a phylogenetic tree that has branch lengths proportional to the
amount of character change.[13]
Chronogram[edit]

A chronogram of Lepidoptera.[14] In this phylogenetic tree type, branch lengths are proportional
to geological time.

A chronogram is a phylogenetic tree that explicitly represents time through its

branch lengths.[15]
Dahlgrenogram[edit]
A Dahlgrenogram is a diagram representing a cross section of a phylogenetic
tree
Phylogenetic network[edit]
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[edit]

A spindle diagram, showing the evolution of the vertebrates at class level, width of spindles
indicating number of families. Spindle diagrams are often used in evolutionary taxonomy.
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]
Coral of life[edit]

The Coral of Life

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[edit]
Main article: Computational phylogenetics
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.
[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, 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[edit]
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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[edit]

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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 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 morpholo