Editing Phylogenetic tree

{{short description|Branching diagram of evolutionary relationships between organisms}}
{{distinguish|text= [[Philogyny]], the fondness, love or admiration of women}}
{{Evolutionary biology}}

A '''phylogenetic tree''', '''phylogeny''' or '''evolutionary tree''' is a graphical representation which shows the [[evolution]]ary history between a set of [[species]] or [[Taxon|taxa]] during a specific time.<ref name=":0">{{Cite book |last=Khalafvand |first=Tyler |url=https://books.google.com/books?id=uEDEtwEACAAJ |title=Finding Structure in the Phylogeny Search Space |date=2015 |publisher=Dalhousie University |language=en}}</ref><ref name="Felsenstein">Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.</ref> In other words, it is a branching [[diagram]] or a [[tree (graph theory)|tree]] showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating [[common ancestry]]. [[Phylogenetics]] is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. [[computational phylogenetics|Computational phylogenetics (also phylogeny inference)]] focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.<ref name=":0" /><ref name="Felsenstein" />

Phylogenetic trees may be rooted or unrooted. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred [[most recent common ancestor]] of those descendants,<ref>{{Cite journal |last1=Kinene |first1=T. |last2=Wainaina |first2=J. |last3=Maina |first3=S. |last4=Boykin |first4=L. |date=21 April 2016 |title=Rooting Trees, Methods for |journal=Encyclopedia of Evolutionary Biology |pages=489–493 |doi=10.1016/B978-0-12-800049-6.00215-8 |pmc=7149615 |isbn=9780128004265 }}</ref> 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.

== History ==

{{further|Tree of life (biology)}}

The idea of a [[tree of life (biology)|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]] featured a diagrammatic [[Tree of life (biology)|evolutionary "tree"]] in his 1859 book ''[[On the Origin of Species]]''. Over a century later, [[Evolutionary biology|evolutionary biologist]]s still use [[Tree structure|tree diagram]]s to depict [[evolution]] because such diagrams effectively convey the concept that [[speciation]] occurs through the [[Adaptation|adaptive]] and [[randomness|semirandom]] splitting of lineages.

The term ''phylogenetic'', or ''phylogeny'', derives from the two [[ancient greek]] words {{wikt-lang|grc|φῦλον}} ({{grc-transl|φῦλον}}), meaning "race, lineage", and {{wikt-lang|grc|γένεσις}} ({{grc-transl|γένεσις}}), meaning "origin, source".<ref>{{Cite book |title=Abrégé du dictionnaire grec français |last=Bailly |first=Anatole |date=1981-01-01 |publisher=Hachette |isbn=978-2010035289 |location=Paris |oclc=461974285 }}</ref><ref>{{Cite web |url=http://www.tabularium.be/bailly/ |title=Greek-french dictionary online |last=Bailly |first=Anatole |website=www.tabularium.be |access-date=March 2, 2018 |url-status=live |archive-url=https://web.archive.org/web/20140421003247/http://www.tabularium.be/bailly/ |archive-date=April 21, 2014 }}</ref>

== Properties ==
=== Rooted tree ===
[[File:Phylogenetic treePureThickBraille.jpg|thumb|upright=1.35 |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 (data structure)|tree]] (see two graphics at top) is a [[directed graph|directed]] tree with a unique node — the root — corresponding to the (usually [[imputation (statistics)|imputed]]) most recent common ancestor of all the entities at the [[leaf node|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 [[Node (computer science)#Nodes and trees|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).{{citation needed|date=June 2024}}

The most common method for rooting trees is the use of an uncontroversial [[outgroup (cladistics)|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]].<ref>{{cite journal |last1=Dang |first1=Cuong Cao |last2=Minh |first2=Bui Quang |last3=McShea |first3=Hanon |last4=Masel |first4=Joanna |last5=James |first5=Jennifer Eleanor |last6=Vinh |first6=Le Sy |last7=Lanfear |first7=Robert |title=nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models |journal=Systematic Biology |date=9 February 2022 |volume=71 |issue=5 |pages=1110–1123 |doi=10.1093/sysbio/syac007|pmid=35139203 |pmc=9366462 }}</ref>

=== Unrooted tree ===
[[File:MyosinUnrootedTree.jpg|thumb|upright=1.35|An unrooted phylogenetic tree for [[myosin]], a [[gene family|superfamily]] of [[protein]]s<ref name=Hodge_2000>{{cite journal|vauthors=Hodge T, Cope M |title=A myosin family tree|journal=J Cell Sci|volume=113|issue=19|pages=3353–4|date=1 October 2000|doi=10.1242/jcs.113.19.3353|url=http://jcs.biologists.org/cgi/content/full/113/19/3353|pmid=10984423|url-status=live|archive-url=https://web.archive.org/web/20070930043742/http://jcs.biologists.org/cgi/content/full/113/19/3353|archive-date=30 September 2007}}</ref>]]

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.<ref>{{cite web |url=https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html |title="Tree" Facts: Rooted versus Unrooted Trees |access-date=2014-05-26 |url-status=live |archive-url=https://web.archive.org/web/20140414030413/http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo9.html |archive-date=2014-04-14 }}</ref> Rooted trees can be generated from unrooted ones by inserting a root. 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]].<!--- THIS REF IS ____ <ref name=Maher_2002>{{cite journal |author=Maher BA |title=Uprooting the Tree of Life |journal=The Scientist |volume=16 |issue=2 |pages=90–95 |year=2002 |url=http://www.the-scientist.com/yr2002/sep/research1_020916.html |url-status=live |archive-url=https://web.archive.org/web/20031002231607/http://www.the-scientist.com/yr2002/sep/research1_020916.html |archive-date=2003-10-02 |bibcode=2000SciAm.282b..90D |doi=10.1038/scientificamerican0200-90 |pmid=10710791}}</ref> I HOPE THIS ONE IS BETTER---><ref>{{cite journal |author=W. Ford Doolittle |title=Uprooting the Tree of Life |journal=Scientific American |volume=282 |issue=2 |pages=90–95 |year=2002 |bibcode=2000SciAm.282b..90D |doi=10.1038/scientificamerican0200-90 |pmid=10710791 |quote=''No abstract available''}}</ref>

=== Bifurcating versus multifurcating ===
Both rooted and unrooted trees can be either [[bifurcation theory|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.{{citation needed|date=June 2024}}

=== 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,<ref>{{cite journal |last1=van Oven |first1=Mannis |last2=Kayser |first2=Manfred |title=Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation |journal=Human Mutation |date=2009 |volume=30 |issue=2 |pages=E386–E394 |doi=10.1002/humu.20921 |pmid=18853457 |s2cid=27566749 |ref=phylotree|doi-access=free }}</ref> feature internal nodes labeled with inferred ancestral haplotypes.

=== Enumerating trees ===
[[File:Number of trees as a function of the number of leaves.svg|thumb|upright=1.35|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 scale|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:

:<math> (2n-3)!! = \frac{(2n-3)!}{2^{n-2}(n-2)!} </math> for <math>n \ge 2</math>, <math>n</math> represents the number of leaf nodes.<ref name="Felsenstein1978">{{Cite journal |last=Felsenstein |first=Joseph |date=1978-03-01 |title=The Number of Evolutionary Trees |url=https://academic.oup.com/sysbio/article/27/1/27/1626689 |journal=Systematic Biology |language=en |volume=27 |issue=1 |pages=27–33 |doi=10.2307/2412810 |issn=1063-5157 |jstor=2412810}}</ref>

For bifurcating labeled trees, the total number of unrooted trees is:<ref name="Felsenstein1978"/>

:<math> (2n-5)!! = \frac{(2n-5)!}{2^{n-3}(n-3)!} </math> for <math>n \ge 3</math>.

Among labeled bifurcating trees, the number of unrooted trees with <math>n</math> leaves is equal to the number of rooted trees with <math>n-1</math> leaves.<ref name="Felsenstein"/>

The number of rooted trees grows quickly as a function of the number of tips. For 10 tips, there are more than <math>34 \times 10^6</math> possible bifurcating trees, and the number of multifurcating trees rises faster, with ca. 7 times as many of the latter as of the former.

{| class=wikitable sortable style=text-align:right
|+ Counting trees.<ref name="Felsenstein1978"/>
! Labeled<br>leaves !! Binary<br>unrooted trees !! Binary<br>rooted trees !! Multifurcating<br>rooted trees !! All possible<br>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.<ref>{{cite web|last1=Fox|first1=Emily|title=The dendrogram|url=https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram|website=coursea|access-date=28 September 2017|url-status=live|archive-url=https://web.archive.org/web/20170928060157/https://www.coursera.org/learn/ml-clustering-and-retrieval/lecture/MfcBU/the-dendrogram|archive-date=28 September 2017}}</ref>
[[File:Phylogenetic tree of dogs.png|thumb|upright=1.35|Dendrogram of the phylogeny of some dog breeds]]

=== 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.<ref>{{Cite journal |last=Mayr |first=Ernst |date=2009-04-27 |title=Cladistic analysis or cladistic classification? |journal=Journal of Zoological Systematics and Evolutionary Research |language=en |volume=12 |issue=1 |pages=94–128 |doi=10.1111/j.1439-0469.1974.tb00160.x|doi-access=free }}</ref><!--Note that cladograms may be constructed using cladistic methods, or any other type of method -- for example, blind guesswork.-->

=== Phylogram ===
A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change.<ref>{{cite journal |first1=Antonio |last1=Soares |first2=Ricardo |last2=Râbelo |first3=Alexandre |last3=Delbem |title=Optimization based on phylogram analysis |journal=Expert Systems with Applications |volume=78 |year=2017 |pages=32–50 |issn=0957-4174 |doi=10.1016/j.eswa.2017.02.012}}</ref>

=== Chronogram ===
A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths.<ref name="Santamaria2009">{{Cite journal |last1=Santamaria |first1=R. |last2=Theron |first2=R. |date=2009-05-26 |title=Treevolution: visual analysis of phylogenetic trees |journal=Bioinformatics |volume=25 |issue=15 |pages=1970–1971 |doi=10.1093/bioinformatics/btp333 |pmid=19470585 |doi-access=free}}</ref>
[[File:Phylogenetic chart of Lepidoptera chronogram.svg|thumb |upright=1.35|A chronogram of [[Lepidoptera]].<ref>{{Cite journal |last1=Labandeira |first1=C. C. |last2=Dilcher |first2=D. L. |last3=Davis |first3=D. R. |last4=Wagner |first4=D. L. |date=1994-12-06 |title=Ninety-seven million years of angiosperm-insect association: paleobiological insights into the meaning of coevolution |journal=Proceedings of the National Academy of Sciences |language=en |volume=91 |issue=25 |pages=12278–12282 |doi=10.1073/pnas.91.25.12278 |issn=0027-8424 |pmc=45420 |pmid=11607501 |bibcode=1994PNAS...9112278L |doi-access=free}}</ref> In this phylogenetic tree type, branch lengths are proportional to geological time.]]

=== Dahlgrenogram ===
A [[Rolf Dahlgren|Dahlgrenogram]] is a diagram representing a cross section of a phylogenetic tree.{{citation needed|date=June 2024}}

=== Phylogenetic network ===
A [[phylogenetic network]] is not strictly speaking a tree, but rather a more general [[Graph (discrete mathematics)|graph]], or a [[directed acyclic graph]] in the case of rooted networks. They are used to overcome some of the [[#Limitations of phylogenetic analysis|limitations]] inherent to trees.

=== Spindle diagram ===
[[File:Spindle diagram.jpg|thumb|upright=1.35|A spindle diagram, showing the evolution of the [[vertebrate]]s 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]].<ref name="palaeos">{{cite web |url=http://palaeos.com/systematics/evolutionary/spindle_diagram.html |title=Evolutionary systematics: Spindle Diagrams |date=2014-11-10 |website=Palaeos.com |access-date=2019-11-07 }}</ref>
It represents taxonomic diversity (horizontal width) against [[Geologic time scale|geological time]] (vertical axis) in order to reflect the variation of abundance of various taxa through time.
A spindle diagram is not an evolutionary tree:<ref name="3lbmonkeybrain">{{cite web |url=https://3lbmonkeybrain.blogspot.com/2007/11/trees-bubbles-and-hooves.html |title= Trees, Bubbles, and Hooves |date=2007-11-21 |website=A Three-Pound Monkey Brain — Biology, programming, linguistics, phylogeny, systematics ... |access-date=2019-11-07 }}</ref> the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon<ref name="palaeos"/> and have the disadvantage of involving the [[paraphyly]] of the parental group.<ref name="Podani2019">{{Cite journal|last=Podani|first=János|date=2019-06-01|title=The Coral of Life|journal=Evolutionary Biology|language=en|volume=46|issue=2|pages=123–144|doi=10.1007/s11692-019-09474-w|issn=1934-2845|doi-access=free|bibcode=2019EvBio..46..123P |hdl=10831/46308|hdl-access=free}}</ref>
This type of diagram is no longer used in the form originally proposed.<ref name="Podani2019"/>

=== Coral of life ===
{{Main|Coral of life}}
[[File:The Coral Of Life Prototype.svg|thumb|upright=1.35|The Coral of Life]]
Darwin<ref name="notebook">{{cite book |last1=Darwin |first1=Charles |title=Notebook B. |date=1837 |page=25 }}</ref> also mentioned that the ''coral'' may be a more suitable metaphor than the ''tree''. Indeed, [[Coral of life|phylogenetic corals]] are useful for portraying past and present life, and they have some advantages over trees ([[Anastomosis|anastomoses]] allowed, etc.).<ref name="Podani2019"/>

== Construction ==
{{Main|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 alignment]]s, 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 inference|Bayesian framework]], and apply an explicit model of evolution to phylogenetic tree estimation.<ref name="Felsenstein" /> Identifying the optimal tree using many of these techniques is [[NP-hard]],<ref name="Felsenstein" /> so [[heuristic]] search and [[Optimization (mathematics)|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:<ref>{{cite journal | last1 = Penny | first1 = D. | last2 = Hendy | first2 = M. D. | last3 = Steel | first3 = M. A. | author3-link=Mike Steel (mathematician) | year = 1992 | title = Progress with methods for constructing evolutionary trees | journal = Trends in Ecology and Evolution | volume = 7 | issue = 3| pages = 73–79 | doi=10.1016/0169-5347(92)90244-6| pmid = 21235960 | bibcode = 1992TEcoE...7...73P }}</ref>
* 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]].<ref>A. Dress, [[Katharina T. Huber|K. T. Huber]], and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. ''Documenta Mathematica'' ''LSU 2001'': 121–139</ref>

=== 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|Nexus file format]]<ref name=":1">{{Cite web |title=Tree Formats |url=https://evomics.org/resources/tree-formats/ |access-date=2025-03-29 |website=Evolution and Genomics |language=en-US}}</ref>
* [[Newick format]]<ref name=":1" />

== Limitations of phylogenetic analysis ==
{{More citations needed section|date=October 2012}}

Although phylogenetic trees produced on the basis of sequenced [[gene]]s or [[genome|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 [[Falsifiability|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 [[signal noise|noisy]];<ref name=Townsend_2012>{{cite journal |vauthors=Townsend JP, Su Z, Tekle Y |title=Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny |journal=Genetics |volume=61 |issue=5 |pages=835–849 |year=2012 |doi=10.1093/sysbio/sys036 |pmid=22389443 |doi-access= }}</ref> the analysis can be confounded by [[genetic recombination]],<ref name=Arenas_2010>{{cite journal |vauthors=Arenas M, Posada D |title=The effect of recombination on the reconstruction of ancestral sequences |journal=Genetics |volume=184 |issue=4 |pages=1133–1139 |year=2010 |doi=10.1534/genetics.109.113423 |pmid=20124027 |pmc=2865913 }}</ref> [[horizontal gene transfer]],<ref name=Woese_2002>{{cite journal |author=Woese C |title=On the evolution of cells |journal=Proc Natl Acad Sci USA |volume=99 |issue=13 |pages=8742–7 |year=2002 |pmid=12077305 |doi=10.1073/pnas.132266999 |pmc=124369|bibcode = 2002PNAS...99.8742W |doi-access=free }}</ref> [[Hybrid (biology)|hybrid]]isation between species that were not nearest neighbors on the tree before hybridisation takes place, and [[conserved sequence]]s.

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 [[Genetic recombination|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),<ref>{{cite journal |doi=10.1016/j.gene.2019.143967 |pmid=31279710 |title=Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group |journal=Gene |volume=713 |pages=143967 |year=2019 |author1=Parhi, J. |author2=Tripathy, P.S. |author3=Priyadarshi, H. |author4=Mandal, S.C. |author5=Pandey, P.K. |s2cid=195828782 }}</ref> or genes that would be expected to evolve under different selective regimes, so that [[homoplasy]] (false [[homology (biology)|homology]]) would be unlikely to result from natural selection.

When extinct species are included as [[leaf node|terminal node]]s 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 [[ancient DNA|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 network]]s 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==
{{Portal|Evolutionary biology}}
{{col div|colwidth=20em}}
* [[Clade]]
* [[Cladistics]]
* [[Computational phylogenetics]]
* [[Evolutionary biology]]
* [[Evolutionary taxonomy]]
* [[Generalized tree alignment]]
* [[List of phylogenetics software]]
* [[List of phylogenetic tree visualization software]]
* [[PANDIT (database)|PANDIT]], a biological database covering protein domains
* [[Phylogenetic comparative methods]]
* [[Phylogenetic reconciliation]]
* [[Taxonomic rank]]
* [[Tokogeny]]
{{colend}}

==References==<!-- MolPhylEvol46:375;48:23,48:313. -->
{{Reflist|2}}

==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, Molecular Evolutionary Genetics Analysis|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==
{{Commons category|Phylogenetic trees}}

=== Images ===
* [https://web.archive.org/web/20120204215457/http://ycc.biosci.arizona.edu/nomenclature_system/fig1.html Human Y-Chromosome 2002 Phylogenetic Tree]
* [http://itol.embl.de/ iTOL: Interactive Tree Of Life]
* [http://picbreeder.com/tol.php Phylogenetic Tree of Artificial Organisms Evolved on Computers] {{Webarchive|url=https://web.archive.org/web/20160222182432/http://picbreeder.com/tol.php |date=2016-02-22 }}
* [https://web.archive.org/web/20110210200039/http://phylogram.org/ Miyamoto and Goodman's Phylogram of Eutherian Mammals]

===General===
* An overview of different methods of tree visualization is available at {{Cite journal | last1 = Page | first1 = R. D. M. | title = Space, time, form: Viewing the Tree of Life | journal = Trends in Ecology & Evolution | volume = 27 | issue = 2 | pages = 113–120 | year = 2011 | doi = 10.1016/j.tree.2011.12.002| pmid = 22209094 }}
* [https://www.onezoom.org/life OneZoom: Tree of Life – all living species as intuitive and zoomable fractal explorer (responsive design)]
* [http://www.discoverlife.org/tree Discover Life] An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project
* [https://web.archive.org/web/20071114093618/http://www.ohiou.edu/phylocode/index.html PhyloCode]
* [http://webarchive.loc.gov/all/20011109204837/http://www.mrc-lmb.cam.ac.uk/myosin/trees/trees.html A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree]
* [http://tolweb.org/tree Tree of Life Web Project]
* [http://www.trex.uqam.ca Phylogenetic inferring on the T-REX server]
* [https://www.ncbi.nlm.nih.gov/Taxonomy/ NCBI's Taxonomy Database] [https://www.ncbi.nlm.nih.gov/Taxonomy/]
* [https://web.archive.org/web/20140525220921/http://ete.cgenomics.org/ ETE: A Python Environment for Tree Exploration] This is a programming library to analyze, manipulate and visualize phylogenetic trees. [http://www.biomedcentral.com/1471-2105/11/24 Ref.]
* [http://supfam.org/SUPERFAMILY/sTOL A daily-updated tree of (sequenced) life] {{Cite journal | last1 = Fang | first1 = H. | last2 = Oates | first2 = M. E. | last3 = Pethica | first3 = R. B. | last4 = Greenwood | first4 = J. M. | last5 = Sardar | first5 = A. J. | last6 = Rackham | first6 = O. J. L. | last7 = Donoghue | first7 = P. C. J. | last8 = Stamatakis | first8 = A. | last9 = De Lima Morais | first9 = D. A. | last10 = Gough | first10 = J. | title = A daily-updated tree of (sequenced) life as a reference for genome research | doi = 10.1038/srep02015 | journal = Scientific Reports | volume = 3 | year = 2013 | pmid =  23778980| pmc = 6504836| page=2015| bibcode = 2013NatSR...3.2015F }}

{{Phylogenetics}}
{{Origin of life}}
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[[Category:Phylogenetics]]
[[Category:Tree of life (biology)| ]]
[[Category:Trees (data structures)]]