Phylogenetic tree
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A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the
Phylogenetic trees may be rooted or unrooted. In a rooted phylogenetic tree, each node with descendants represents the inferred
History
The idea of a
Charles Darwin featured a diagrammatic evolutionary "tree" in his 1859 book On 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.
The term phylogenetic, or phylogeny, derives from the two
Properties
Rooted tree
A rooted phylogenetic
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. Another method is midpoint rooting, or a tree can also be rooted by using a non-stationary substitution model.[6]
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.[8] 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.[9]
Bifurcating versus multifurcating
Both rooted and unrooted trees can be either
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,[10] feature internal nodes labeled with inferred ancestral haplotypes.
Enumerating trees
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.[11]
For bifurcating labeled trees, the total number of unrooted trees is:[11]
- for .
Among labeled bifurcating trees, the number of unrooted trees with leaves is equal to the number of rooted trees with leaves.[2]
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.
Labeled leaves |
Binary unrooted trees |
Binary rooted trees |
Multifurcating rooted trees |
All possible rooted trees |
---|---|---|---|---|
1 | 1 | 1 | 0 | 1 |
2 | 1 | 1 | 0 | 1 |
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.[12]
Cladogram
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.[13]
Phylogram
A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change.[15]
A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths.[16]
Dahlgrenogram
A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree.
Phylogenetic network
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.[17] 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:[18] the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon[17] and have the disadvantage of involving the paraphyly of the parental group.[19] This type of diagram is no longer used in the form originally proposed.[19]
Coral of life
Darwin[20] 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.).[19]
Construction
Phylogenetic trees composed with a nontrivial number of input sequences are constructed using
Tree-building methods can be assessed on the basis of several criteria:[21]
- 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.[22]
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
Limitations of phylogenetic analysis
This section needs additional citations for verification. (October 2012) |
Although phylogenetic trees produced on the basis of sequenced
Also, there are problems in basing an analysis on a single type of character, such as a single
When extinct species are included as
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
- Cladistics
- Computational phylogenetics
- Evolutionary biology
- Evolutionary taxonomy
- Generalized tree alignment
- List of phylogenetics software
- List of phylogenetic tree visualization software
- PANDIT, a biological database covering protein domains
- Phylogenetic comparative methods
- Phylogenetic reconciliation
- Taxonomic rank
References
- ^ a b Khalafvand, Tyler (2015). Finding Structure in the Phylogeny Search Space. Dalhousie University.
- ^ a b c d e Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
- PMC 7149615.
- OCLC 461974285.
- ^ Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Archived from the original on April 21, 2014. Retrieved March 2, 2018.
- PMID 35139203.
- from the original on 30 September 2007.
- ^ ""Tree" Facts: Rooted versus Unrooted Trees". Archived from the original on 2014-04-14. Retrieved 2014-05-26.
- PMID 10710791.
No abstract available
- S2CID 27566749.
- ^ JSTOR 2412810.
- ^ Fox, Emily. "The dendrogram". coursea. Archived from the original on 28 September 2017. Retrieved 28 September 2017.
- ^ Mayr, Ernst (1974)"Cladistic analysis or cladistic classification?". Journal of Zoological Systematics and Evolutionary Research. 12: 94–128. doi:10.1111/j.1439-0469.1974.tb00160.x.
- PMID 11607501.
- ISSN 0957-4174.
- PMID 19470585.
- ^ a b "Evolutionary systematics: Spindle Diagrams". Palaeos.com. 2014-11-10. Retrieved 2019-11-07.
- ^ "Trees, Bubbles, and Hooves". A Three-Pound Monkey Brain — Biology, programming, linguistics, phylogeny, systematics …. 2007-11-21. Retrieved 2019-11-07.
- ^ ISSN 1934-2845.
- ^ Darwin, Charles (1837). Notebook B. p. 25.
- PMID 21235960.
- ^ A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. Documenta Mathematica LSU 2001: 121-139
- PMID 22389443.
- PMID 20124027.
- PMID 12077305.
- S2CID 195828782.
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.
- Jan Sapp, The New Foundations of Evolution: On the Tree of Life, 2009, Oxford University Press, New York.
External links
Images
- Human Y-Chromosome 2002 Phylogenetic Tree
- iTOL: Interactive Tree Of Life
- Phylogenetic Tree of Artificial Organisms Evolved on Computers Archived 2016-02-22 at the Wayback Machine
- Miyamoto and Goodman's Phylogram of Eutherian Mammals
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. PMID 22209094.
- OneZoom: Tree of Life – all living species as intuitive and zoomable fractal explorer (responsive design)
- Discover Life An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project
- PhyloCode
- A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree
- 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) life 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". Scientific Reports. 3: 2015. PMID 23778980.