Phylogenetic tree

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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. Phylogenetic tree_sentence_0

All life on Earth is part of a single phylogenetic tree, indicating common ancestry. Phylogenetic tree_sentence_1

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. Phylogenetic tree_sentence_2

Each node is called a taxonomic unit. Phylogenetic tree_sentence_3

Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Phylogenetic tree_sentence_4

Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. Phylogenetic tree_sentence_5

Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. Phylogenetic tree_sentence_6

History Phylogenetic tree_section_0

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). Phylogenetic tree_sentence_7

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). Phylogenetic tree_sentence_8

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. Phylogenetic tree_sentence_9

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. Phylogenetic tree_sentence_10

Over time, species classification has become less static and more dynamic. Phylogenetic tree_sentence_11

The term phylogenetic, or phylogeny, derives from the two ancient greek words (phûlon), meaning "race, lineage", and (génesis), meaning "origin, source". Phylogenetic tree_sentence_12

Properties Phylogenetic tree_section_1

Rooted tree Phylogenetic tree_section_2

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. Phylogenetic tree_sentence_13

The root node does not have a parent node, but serves as the parent of all other nodes in the tree. Phylogenetic tree_sentence_14

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). Phylogenetic tree_sentence_15

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. Phylogenetic tree_sentence_16

Unrooted tree Phylogenetic tree_section_3

Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. Phylogenetic tree_sentence_17

They do not require the ancestral root to be known or inferred. Phylogenetic tree_sentence_18

Unrooted trees can always be generated from rooted ones by simply omitting the root. Phylogenetic tree_sentence_19

By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. Phylogenetic tree_sentence_20

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. Phylogenetic tree_sentence_21

Bifurcating versus multifurcating Phylogenetic tree_section_4

Both rooted and unrooted trees can be either bifurcating or multifurcating. Phylogenetic tree_sentence_22

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. Phylogenetic tree_sentence_23

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. Phylogenetic tree_sentence_24

Labeled versus unlabeled Phylogenetic tree_section_5

Both rooted and unrooted trees can be either labeled or unlabeled. Phylogenetic tree_sentence_25

A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. Phylogenetic tree_sentence_26

Some sequence-based trees built from a small genomic locus, such as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes. Phylogenetic tree_sentence_27

Enumerating trees Phylogenetic tree_section_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. Phylogenetic tree_sentence_28

The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. Phylogenetic tree_sentence_29

For bifurcating labeled trees, the total number of rooted trees is: Phylogenetic tree_sentence_30

For bifurcating labeled trees, the total number of unrooted trees is: Phylogenetic tree_sentence_31

Phylogenetic tree_table_general_0

Counting trees.Phylogenetic tree_table_caption_0
Labeled

leavesPhylogenetic tree_header_cell_0_0_0

Binary

unrooted treesPhylogenetic tree_header_cell_0_0_1

Binary

rooted treesPhylogenetic tree_header_cell_0_0_2

Multifurcating

rooted treesPhylogenetic tree_header_cell_0_0_3

All possible

rooted treesPhylogenetic tree_header_cell_0_0_4

1Phylogenetic tree_cell_0_1_0 1Phylogenetic tree_cell_0_1_1 1Phylogenetic tree_cell_0_1_2 0Phylogenetic tree_cell_0_1_3 1Phylogenetic tree_cell_0_1_4
2Phylogenetic tree_cell_0_2_0 1Phylogenetic tree_cell_0_2_1 1Phylogenetic tree_cell_0_2_2 0Phylogenetic tree_cell_0_2_3 1Phylogenetic tree_cell_0_2_4
3Phylogenetic tree_cell_0_3_0 1Phylogenetic tree_cell_0_3_1 3Phylogenetic tree_cell_0_3_2 1Phylogenetic tree_cell_0_3_3 4Phylogenetic tree_cell_0_3_4
4Phylogenetic tree_cell_0_4_0 3Phylogenetic tree_cell_0_4_1 15Phylogenetic tree_cell_0_4_2 11Phylogenetic tree_cell_0_4_3 26Phylogenetic tree_cell_0_4_4
5Phylogenetic tree_cell_0_5_0 15Phylogenetic tree_cell_0_5_1 105Phylogenetic tree_cell_0_5_2 131Phylogenetic tree_cell_0_5_3 236Phylogenetic tree_cell_0_5_4
6Phylogenetic tree_cell_0_6_0 105Phylogenetic tree_cell_0_6_1 945Phylogenetic tree_cell_0_6_2 1,807Phylogenetic tree_cell_0_6_3 2,752Phylogenetic tree_cell_0_6_4
7Phylogenetic tree_cell_0_7_0 945Phylogenetic tree_cell_0_7_1 10,395Phylogenetic tree_cell_0_7_2 28,813Phylogenetic tree_cell_0_7_3 39,208Phylogenetic tree_cell_0_7_4
8Phylogenetic tree_cell_0_8_0 10,395Phylogenetic tree_cell_0_8_1 135,135Phylogenetic tree_cell_0_8_2 524,897Phylogenetic tree_cell_0_8_3 660,032Phylogenetic tree_cell_0_8_4
9Phylogenetic tree_cell_0_9_0 135,135Phylogenetic tree_cell_0_9_1 2,027,025Phylogenetic tree_cell_0_9_2 10,791,887Phylogenetic tree_cell_0_9_3 12,818,912Phylogenetic tree_cell_0_9_4
10Phylogenetic tree_cell_0_10_0 2,027,025Phylogenetic tree_cell_0_10_1 34,459,425Phylogenetic tree_cell_0_10_2 247,678,399Phylogenetic tree_cell_0_10_3 282,137,824Phylogenetic tree_cell_0_10_4

Special tree types Phylogenetic tree_section_7

Construction Phylogenetic tree_section_8

Main article: Computational phylogenetics Phylogenetic tree_sentence_32

Phylogenetic trees composed with a nontrivial number of input sequences are constructed using computational phylogenetics methods. Phylogenetic tree_sentence_33

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. Phylogenetic tree_sentence_34

Many sequence alignment methods such as ClustalW also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. Phylogenetic tree_sentence_35

Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). Phylogenetic tree_sentence_36

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. Phylogenetic tree_sentence_37

Identifying the optimal tree using many of these techniques is NP-hard, so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data. Phylogenetic tree_sentence_38

Tree-building methods can be assessed on the basis of several criteria: Phylogenetic tree_sentence_39

Phylogenetic tree_unordered_list_0

  • efficiency (how long does it take to compute the answer, how much memory does it need?)Phylogenetic tree_item_0_0
  • power (does it make good use of the data, or is information being wasted?)Phylogenetic tree_item_0_1
  • consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)Phylogenetic tree_item_0_2
  • robustness (does it cope well with violations of the assumptions of the underlying model?)Phylogenetic tree_item_0_3
  • falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)Phylogenetic tree_item_0_4

Tree-building techniques have also gained the attention of mathematicians. Phylogenetic tree_sentence_40

Trees can also be built using T-theory. Phylogenetic tree_sentence_41

File formats Phylogenetic tree_section_9

Images Phylogenetic tree_section_10

Phylogenetic tree_unordered_list_1

  • Phylogenetic tree_item_1_5
  • Phylogenetic tree_item_1_6
  • Phylogenetic tree_item_1_7
  • Phylogenetic tree_item_1_8

General Phylogenetic tree_section_11

Phylogenetic tree_unordered_list_2

  • 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:. PMID .Phylogenetic tree_item_2_9
  • Phylogenetic tree_item_2_10
  • An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life ProjectPhylogenetic tree_item_2_11
  • Phylogenetic tree_item_2_12
  • Phylogenetic tree_item_2_13
  • Phylogenetic tree_item_2_14
  • Phylogenetic tree_item_2_15
  • Phylogenetic tree_item_2_16
  • This is a programming library to analyze, manipulate and visualize phylogenetic trees.Phylogenetic tree_item_2_17
  • 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). . Scientific Reports. 3: 2015. Bibcode:. doi:. PMC . PMID .Phylogenetic tree_item_2_18


Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Phylogenetic tree.