View source for Tree of life (biology)

{{short description|Model for the evolution of species}}
{{good article}}
{{use British English |date=November 2022}}
{{use dmy dates |date=November 2022}}
The '''tree of life''' or '''universal tree of life''' is a [[metaphor]], [[conceptual model]], and research tool used to explore the [[evolution]] of life and describe the relationships between [[organism]]s, both living and extinct, as described in a famous passage in [[Charles Darwin]]'s ''[[On the Origin of Species]]'' (1859).<ref name="Mindell 2013">{{cite journal |last=Mindell |first=D. P. |title=The Tree of Life: Metaphor, Model, and Heuristic Device |journal=Systematic Biology |date=3 January 2013 |volume=62 |issue=3 |pages=479–489 |doi=10.1093/sysbio/sys115 |pmid=23291311 |doi-access=free }}</ref>

{{Blockquote
 |text=The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.
 |author=Charles Darwin<ref name="origin">{{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |title=On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life |date=1859 |publisher=John Murray |location=London |page=129 |edition=First Edition, First Thousand |chapter-url=http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=image&pageseq=1 |chapter=Four: Natural Selection; or the Survival of the Fittest}}</ref>}}

Tree diagrams originated in the [[Middle Ages|medieval era]] to represent [[family tree|genealogical relationships]]. [[Phylogenetic tree]] diagrams in the evolutionary sense date back to the mid-nineteenth century.

The term [[phylogeny]] for the evolutionary relationships of [[species]] through time was coined by [[Ernst Haeckel]], who went further than [[Charles Darwin|Darwin]] in proposing [[Phylogenetics|phylogenic]] histories of life. In contemporary usage, ''tree of life'' refers to the compilation of comprehensive phylogenetic databases rooted at the [[last universal common ancestor]] of life on [[Earth]]. Two public databases for the tree of life are ''[[TimeTree]]'', for phylogeny and divergence times, and the ''[[Open Tree of Life]]'', for phylogeny.

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== History ==

=== Early natural classification ===

{{further|History of evolutionary thought}}

[[File:Edward Hitchcock Paleontological Chart.jpg|thumb|upright=1.6|[[Edward Hitchcock]]'s fold-out paleontological chart in his 1840 ''Elementary Geology'']]

Although tree-like diagrams have long been used to organise knowledge, and although branching diagrams known as ''claves'' ("keys") were omnipresent in eighteenth-century [[natural history]], it appears that the earliest tree diagram of natural order was the 1801 "Arbre botanique" (Botanical Tree) of the French schoolteacher and Catholic priest [[Augustin Augier]].<ref name="Hellström 2019">{{cite journal |last=Hellström |first=Petter |url=https://www.academia.edu/40660349 |title=Trees of Knowledge. Science and the Shape of Genealogy (doctoral thesis) |journal=Uppsala: Acta Universitatis Upsalienses |publisher=Acta Universitatis Upsalienses |year=2019 |location=Uppsala |language=en}}</ref><ref>{{Cite book |last=Augier |first=Augustin |author-link=Augustin Augier |url=https://www.biodiversitylibrary.org/bibliography/87725 |title=Essai d'une nouvelle classification des végétaux: conforme à l'ordre que la nature paroît avoir suivi dans le règne végétal; d'ou résulte une méthode qui conduit a la connoissance des plantes & de leurs rapports naturels |publisher=Bruyset Ainé et Comp. |year=1801 |location=Lyons }}</ref> Yet, although Augier discussed his tree in distinctly genealogical terms, and although his design clearly mimicked the visual conventions of a contemporary [[family tree]], his tree did not include any evolutionary or temporal aspect. Consistent with Augier's priestly vocation, the Botanical Tree showed rather the perfect order of nature as instituted by God at the moment of Creation.<ref>{{cite journal |last1=Hellström |first1=Petter |last2=Gilles |first2=André |last3=Philippe |first3=Marc |date=2017 |title=Life and works of Augustin Augier de Favas (1758–1825), author of "Arbre botanique" (1801) |url=https://www.academia.edu/32184058 |journal=Archives of Natural History |volume=44 |pages=43–62 |doi=10.3366/anh.2017.0413 }}</ref>

In 1809, Augier's more famous compatriot [[Jean-Baptiste Lamarck]] (1744–1829), who was acquainted with Augier's "Botanical Tree",<ref>{{cite journal |last1=Hellström |first1=Petter |last2=Gilles |first2=André |last3=Philippe |first3=Marc |date=2017 |title=Augustin Augier's Botanical Tree. Transcripts and translations of two unknown sources |url=https://www.academia.edu/33403519 |journal=[[Huntia (journal)|Huntia]] |volume=16 |pages=17–38}}</ref> included a branching diagram of animal species in his ''[[Philosophie Zoologique|Philosophie zoologique]]''.<ref>{{cite book |last=Lamarck |first=Jean-Baptiste |author-link=Jean-Baptiste Lamarck |title=Philosophie zoologique |volume=2 |date=1809 |publisher=Dentu |location=Paris, France |page=463 |language=fr }} Available at: [https://web.archive.org/web/20191014012720/http://lhldigital.lindahall.org/cdm/ref/collection/darwin/id/458 Linda Hall Library, University of Missouri (Kansas City, Missouri, USA)]</ref> Unlike Augier, however, Lamarck did not discuss his diagram in terms of a genealogy or a tree, but instead named it a ''tableau'' ("depiction").<ref name="Hellström 2012"/> Lamarck believed in the transmutation of life forms, but he did not believe in common descent; instead he believed that life developed in parallel lineages (repeated, spontaneous generation) advancing from more simple to more complex.<ref>{{cite book |last=Bowler |first=Peter J. |author-link=Peter J. Bowler |year=2003 |title=Evolution. The History of an Idea |edition=Third |publisher=University of California Press |location=Berkeley |isbn=978-0520236936 |pages=90–91}}</ref>

In 1840, the American geologist [[Edward Hitchcock]] (1793–1864) published the first tree-like [[paleontology]] chart in his ''Elementary Geology'', with two separate trees for the plants and the animals. These are crowned (graphically) with the [[Palmae|Palms]] and Man.<ref>{{cite journal |last1=Archibald |first1=J. David |year=2009 |title=Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life' |doi=10.1007/s10739-008-9163-y |pmid=20027787 |journal=Journal of the History of Biology |volume=42 |issue=3 |pages=561–592 |citeseerx=10.1.1.688.7842 |s2cid=16634677 }}</ref>

The first edition of [[Robert Chambers (publisher, born 1802)|Robert Chambers]]' ''[[Vestiges of the Natural History of Creation]]'', published anonymously in 1844 in England, contained a tree-like diagram in the chapter "Hypothesis of the development of the vegetable and animal kingdoms".{{sfnp |Chambers |1844 |p=[https://archive.org/details/vestigesofnatura00unse/page/212 212]}} It shows a model of [[Embryology|embryological]] development where fish (F), reptiles (R), and birds (B) represent branches from a path leading to mammals (M). In the text this branching tree idea is tentatively applied to the history of life on earth: "there may be branching".<ref>{{cite book |last=Chambers |first=Robert |title=Vestiges of the Natural History of Creation |date=1844 |publisher=John Churchill |location=London, England |url=https://archive.org/details/vestigesofnatura00unse/page/190 |page=191 }}</ref>

In 1858, a year before Darwin's ''Origin'', the paleontologist [[Heinrich Georg Bronn]] (1800–1862) published a hypothetical tree labelled with letters.<ref>{{cite book |last1=Bronn |first1=H. G. |title=Untersuchungen über die Entwicklungs-Gesetze der organischen Welt während der Bildungs-Zeit unserer Erd-Oberfläche |trans-title=Investigations of the laws of the development of the organic world during the period of formation of our Earth's surface |date=1858 |publisher=F. Schweizerbart |location=Stuttgart, (Germany) |pages=481–482 |url=https://books.google.com/books?id=J6WCP3J7GIUC&pg=PA481 |language=de}}</ref> Although not a creationist, Bronn did not propose a mechanism of change.<ref>{{cite journal |last1=Archibald |first1=J. David |year=2009 |title=Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life' |doi=10.1007/s10739-008-9163-y |pmid=20027787 |journal=[[Journal of the History of Biology]] |volume=42 |issue=3 |page=568 |citeseerx=10.1.1.688.7842 |s2cid=16634677 }}</ref>

<gallery mode="packed" widths="180" heights="275">
File:Augier tree of life.jpg|[[Augustin Augier]]'s 1801 ''Arbre botanique'' ("Botanical Tree")<ref name="Hellström 2019"/>
File:Lamark's depiction of the origins of the animals.gif|[[Jean-Baptiste Lamarck]]'s 1809 depiction of the origins of animal groups in his ''[[Philosophie zoologique]]'' with branching evolutionary paths, not considered an evolutionary tree
File:Vestiges dev diag labelled.svg|Diagram in [[Robert Chambers (publisher born 1802)|Robert Chambers]]'s 1844 ''[[Vestiges of the Natural History of Creation]]''
</gallery>

=== Darwin ===

{{further|Evolution|Common descent}}

[[Charles Darwin]] (1809–1882) used the metaphor of a "tree of life" to conceptualise his theory of evolution. In ''[[On the Origin of Species]]'' (1859) he presented an abstract diagram of a portion of a larger [[timetree]] for species of an unnamed large [[genus]] (see figure). On the horizontal base line hypothetical species within this genus are labelled A – L and are spaced irregularly to indicate how distinct they are from each other, and are above broken lines at various angles suggesting that they have diverged from one or more common ancestors. On the vertical axis divisions labelled I – XIV each represent a thousand generations. From A, diverging lines show branching descent producing new varieties, some of which become extinct, so that after ten thousand generations descendants of A have become distinct new varieties or even sub-species a<sup>10</sup>, f<sup>10</sup>, and m<sup>10</sup>. Similarly, the descendants of I have diversified to become the new varieties w<sup>10</sup> and z<sup>10</sup>. The process is extrapolated for a further four thousand generations so that the descendants of A and I become fourteen new species labelled a<sup>14</sup> to z<sup>14</sup>. While F has continued for fourteen thousand generations relatively unchanged, species B,C,D,E,G,H,K and L have gone extinct. In Darwin's own words: "Thus the small differences distinguishing varieties of the same species, will steadily tend to increase till they come to equal the greater differences between species of the same genus, or even of distinct genera."{{sfnp|Darwin|1859|pp=[http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F373&pageseq=131 116–130]}} Darwin's tree is not a tree of life, but rather a small portion created to show the principle of evolution. Because it shows relationships (phylogeny) and time (generations), it is a timetree. In contrast, [[Ernst Haeckel]] illustrated a phylogenetic tree (branching only) in 1866, not scaled to time, and of real species and higher taxa. In his summary to the section, Darwin put his concept in terms of the metaphor of the tree of life:

{{blockquote|The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the [[Platypus|Ornithorhynchus]] or [[South American Lungfish|Lepidosiren]], which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a [[ecological niche|protected station]]. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.|[[Charles Darwin|Darwin]], 1859.{{sfn|Darwin|1859|loc=pp. [http://darwin-online.org.uk/content/frameset?pageseq=147&itemID=F373&viewtype=text 129–130]: {{Source-attribution|inline=y}} }}}}

The meaning and importance of Darwin's use of the tree of life metaphor have been extensively discussed by scientists and scholars. [[Stephen Jay Gould]], for one, has argued that Darwin placed the famous passage quoted above "at a crucial spot in his text", where it marked the conclusion of his argument for natural selection, illustrating both the interconnectedness by descent of organisms as well as their success and failure in the history of life.<ref>{{cite book |last=Gould |first=Stephen Jay |author-link=Stephen Jay Gould |year=1993 |title=Eight Little Piggies |publisher=Jonathan Cape |location=London |isbn=978-0-224-03716-7 |url-access=registration |url=https://archive.org/details/eightlittlepiggi0000goul }} p. 300</ref> [[David Penny]] has written that Darwin did not use the tree of life to describe the relationship between groups of organisms, but to suggest that, as with branches in a living tree, lineages of species competed with and supplanted one another.<ref>{{cite journal |last=Penny |first=D. |year=2011 |title=Darwin's Theory of Descent with Modification, versus the Biblical Tree of Life |journal=PLOS Biology |volume=9 |issue=7 |page=e1001096 |doi=10.1371/journal.pbio.1001096 |pmid=21750664 |pmc=3130011 |doi-access=free }}</ref> Petter Hellström has argued that Darwin consciously named his tree after the biblical [[Tree of life (biblical)|Tree of Life]], as described in [[Genesis creation narrative|Genesis]], thus relating his theory to the religious tradition.<ref name="Hellström 2012">{{cite journal |last1=Hellström |first1=Petter |year=2012 |title=Darwin and the Tree of Life: The Roots the Evolutionary Tree |url=https://www.academia.edu/4613148 |journal=Archives of Natural History |volume=39 |issue=2 |pages=234–252 |doi=10.3366/anh.2012.0092 }}</ref>

<gallery mode="packed" heights="250px">
File:Darwin Tree 1837.png|Page from Darwin's notebooks ({{circa|July 1837}}) with his first sketch of an evolutionary tree, and the words "I think" at the top
File:Origin of Species.svg|Diagram in Darwin's ''[[On the Origin of Species]]'', 1859.<br/>It was the book's only illustration. The letters A–L represent distinct descents. Each horizontal line represents 1000 generations. Descent A has 3 existent species after 10000 generations. Descent I has 2. Descents E, F have 1 each. The other descents have gone extinct.
</gallery>

=== Haeckel ===

[[Ernst Haeckel]] (1834–1919) constructed several trees of life. His first sketch, in the 1860s, shows "''Pithecanthropus alalus''" as the ancestor of ''Homo sapiens''.<ref>{{cite journal |last=Gliboff |first=Sander |title=Ascent, Descent, and Divergence: Darwin and Haeckel on the Human Family Tree |journal=Konturen |date=2014 |volume=6 |page=103 |doi=10.5399/uo/konturen.7.0.3523 |url=http://journals.oregondigital.org/konturen/article/view/3523/3284 |hdl=1794/24398 |hdl-access=free |access-date=27 June 2022 |archive-date=20 November 2022 |archive-url=https://web.archive.org/web/20221120123351/http://journals.oregondigital.org/konturen/article/view/3523/3284 |url-status=dead }}</ref> His 1866 tree of life from ''Generelle Morphologie der Organismen'' shows three kingdoms: Plantae, Protista and Animalia. This has been described as "the earliest 'tree of life' model of [[biodiversity]]".<ref name="Hossfeld Levit 2016">{{cite journal |last1=Hossfeld |first1=Uwe |last2=Levit |first2=Georgy S. |title='Tree of life' took root 150 years ago |journal=Nature |volume=540 |issue=7631 |date=30 November 2016 |doi=10.1038/540038a |pages=38|pmid=27905437 |s2cid=414511 |doi-access=free }}</ref> His 1879 "Pedigree of Man" was published in his 1879 book ''The Evolution of Man''. It traces all life forms to the [[Monera]], and places Man (labelled "{{lang|de|Menschen}}") at the top of the tree.<ref>{{cite web |last1=Carr |first1=Steven M. |title=Haeckel's Tree of Life |url=https://www.mun.ca/biology/scarr/Haeckel_Tree_of_Life.html |publisher=Memorial University of Newfoundland |access-date=27 June 2022 |date=2005}}</ref>

<gallery mode="packed" heights="250px">
File:Ernst Haeckel - Tree of Life.jpg|[[Ernst Haeckel|Haeckel]]'s ''Stammbaum der Primaten'' (1860s)
File:Haeckel arbol bn.png|Haeckel's tree of life in ''Generelle Morphologie der Organismen'' (1866)
File:Tree of life by Haeckel.jpg|The tree of life as seen by Haeckel in ''The Evolution of Man'' (1879)
</gallery>

===Developments since 1990===

{{further|Kingdom (biology)}}

[[File:PhylogeneticTree, Woese 1990.PNG|thumb|upright=2|Universal phylogenetic tree in rooted form, showing the three domains (Woese, Kandler, Wheelis 1990, p. 4578<ref name="Woese_1990" />)]]

In 1990, [[Carl Woese]], [[Otto Kandler]] and [[Mark Wheelis]] proposed a novel "tree of life" consisting of three lines of descent for which they introduced the term [[Domain (biology)|domain]] as the highest rank of classification. They suggested and formally defined the terms [[Bacteria]], [[Archaea]] and [[Eukaryote|Eukarya]] for the three domains of life.<ref name="Woese_1990">{{cite journal |last1=Woese |first1=Carl R. |author-link1=Carl Woese |last2=Kandler |first2=Otto |author-link2=Otto Kandler |last3=Wheelis |first3=Mark L.|author-link3=Mark Wheelis |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=PNAS |volume=87 |issue=12 |pages=4576–4579 |year=1990 |pmid=2112744 |doi=10.1073/pnas.87.12.4576 |pmc=54159 |bibcode=1990PNAS...87.4576W |doi-access=free}}</ref> It was the first tree founded on molecular phylogenetics and microbial evolution as its basis.<ref name="Sapp2009">{{Cite book |last=Sapp |first=Jan A. |url=https://books.google.com/books?id=d7zOviXnbSYC |title=The new foundations of evolution: on the tree of life |publisher=Oxford University Press |year=2009 |isbn=978-0-199-73438-2 |location=New York |author-link=Jan Sapp}}</ref><ref>{{Cite book |last=Harold |first=Franklin M. |url=https://books.google.com/books?id=XjOOBAAAQBAJ&q=In+Search+of+Cell+History |title=In Search of Cell History: The Evolution of Life's Building Blocks |publisher=University of Chicago Press |year=2014 |isbn=978-0-226-17428-0 |location=Chicago, London |pages=35}}</ref> 

The model of a tree is still considered valid for eukaryotic life forms. Trees have been proposed with either four<ref name=Burki2008>{{Cite journal |last1=Burki |first1=Fabien |last2=Shalchian-Tabrizi |first2=Kamran |last3=Pawlowski |first3=Jan |year=2008 |title=Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes |journal=Biology Letters |volume=4 |pages=366–369 |doi=10.1098/rsbl.2008.0224 |name-list-style=amp |pmid=18522922 |issue=4 |pmc=2610160 }}</ref><ref>{{Cite web |url=http://www.apollon.uio.no/vis/art/2007_4/Artikler/The_Tree_of_Life |title=Apollon: The Tree of Life Has Lost a Branch |access-date=23 January 2008 |archive-date=28 October 2011 |archive-url=https://web.archive.org/web/20111028022834/http://www.apollon.uio.no/vis/art/2007_4/Artikler/The_Tree_of_Life |url-status=dead }}</ref> or two supergroups.<ref name=KimGraham2008>{{cite journal |last1=Kim |first1=E. |last2=Graham |first2=L. E. |last3=Redfield |first3=Rosemary Jeanne |author-link3=Rosemary Redfield |editor-last=Redfield |year=2008 |title=EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata |journal=PLOS ONE |volume=3 |issue=7 |pages=e2621 |doi=10.1371/journal.pone.0002621 |pmid=18612431 |pmc=2440802  |doi-access=free |bibcode=2008PLoSO...3.2621K }}</ref> There does not yet appear to be a consensus; in a 2009 review article, Roger and Simpson conclude that "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."<ref>{{Cite journal |last1=Roger |first1=A. J. |last2=Simpson |first2=A. G. B. |year=2009 |title=Evolution: Revisiting the Root of the Eukaryote Tree |journal=Current Biology |volume=19 |issue=4 |pages=R165–7 |doi=10.1016/j.cub.2008.12.032 |pmid=19243692 |s2cid=13172971 |name-list-style=amp |doi-access=free }}</ref>

In 2015, the third version of [[TimeTree]] was released, with 2,274 studies and 50,632 species, represented in a spiral tree of life,<ref name="Hedges 835–845">{{Cite journal |last1=Hedges |first1=S. Blair |last2=Marin |first2=Julie |last3=Suleski |first3=Michael |last4=Paymer |first4=Madeline |last5=Kumar |first5=Sudhir |date=April 2015 |title=Tree of Life Reveals Clock-Like Speciation and Diversification |url=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msv037 |journal=Molecular Biology and Evolution |language=en |volume=32 |issue=4 |pages=835–845 |doi=10.1093/molbev/msv037 |issn=1537-1719 |pmc=4379413 |pmid=25739733}}</ref> free to download.

In 2015, the first draft of the [[Open Tree of Life]] was published, in which information from nearly 500 previously published trees was combined into a single online database, free to browse and download.<ref>{{cite news |last1=Pennisi |first1=Elizabeth |url=https://www.science.org/content/article/first-comprehensive-tree-life-shows-how-related-you-are-millions-species |title=First comprehensive tree of life shows how related you are to millions of species |journal=Science |date=21 September 2015 |doi=10.1126/science.aad4597 |access-date=30 January 2023}}</ref> Another database, ''TimeTree'', helps biologists to evaluate phylogeny and divergence times.<ref>{{cite web |title=TimeTree of Life |url=http://www.timetree.org/ |website=Timetree.org |access-date=27 June 2022}}</ref>

In 2016, a new tree of life (unrooted), summarising the [[evolution]] of all known [[life forms]], was published, illustrating the latest [[gene]]tic findings that the branches were mainly composed of bacteria. The new study incorporated over a thousand newly discovered bacteria and archaea.<ref name="NYT-20160411">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |date=11 April 2016 |title=Scientists Unveil New 'Tree of Life' |work=[[New York Times]] |url=https://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html |access-date=11 April 2016 }}</ref><ref name="TS-20160411">{{Cite web |last=Taylor |first=Ashley P. |title=Branching Out: Researchers create a new tree of life, largely {{sic|comprised|hide=y|of}} mystery bacteria |url=http://www.the-scientist.com/?articles.view/articleNo/45793/title/Branching-Out/ |date=11 April 2016 |work=[[The Scientist (magazine)|The Scientist]] |access-date=11 April 2016}}</ref><ref name="NM-20160411">{{cite journal |last1=Hug |first1=Laura A. |last2=Baker |first2=Brett J. |last3=Anantharaman |first3=Karthik |last4=Brown |first4=Christopher T. |last5=Probst |first5=Alexander J. |last6=Castelle |first6=Cindy J. |last7=Butterfield |first7=Cristina N. |last8=Hernsdorf |first8=Alex W. |last9=Amano |first9=Yuki |last10=Ise |first10=Kotaro |last11=Suzuki |first11=Yohey |last12=Dudek |first12=Natasha |last13=Relman |first13=David A. |last14=Finstad |first14=Kari M. |last15=Amundson |first15=Ronald |display-authors=4 |date=11 April 2016 |title=A new view of the tree of life |journal=[[Nature Microbiology]] |volume=1 |issue=5 |at=16048 |doi=10.1038/nmicrobiol.2016.48 |pmid=27572647 |doi-access=free |last16=Thomas |first16=Brian C. |last17=Banfield |first17=Jillian F.}}</ref>

In 2022, the fifth version of [[TimeTree]] was released, incorporating 4,185 published studies and 148,876 species, representing the largest timetree of life from actual data (non-imputed).<ref>{{Cite journal |last1=Kumar |first1=Sudhir |last2=Suleski |first2=Michael |last3=Craig |first3=Jack M |last4=Kasprowicz |first4=Adrienne E |last5=Sanderford |first5=Maxwell |last6=Li |first6=Michael |last7=Stecher |first7=Glen |last8=Hedges |first8=S Blair |date=2022-08-03 |title=TimeTree 5: An Expanded Resource for Species Divergence Times |url=https://academic.oup.com/mbe/article/doi/10.1093/molbev/msac174/6657692 |journal=Molecular Biology and Evolution |language=en |volume=39 |issue=8 |pages=msac174 |doi=10.1093/molbev/msac174 |issn=0737-4038 |pmc=9400175 |pmid=35932227}}</ref>
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      Please don't try to document recent developments in [[phylogeny]] or the [[Domain (biology)|domain]]s of life here; such things are the subjects of other articles
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==Horizontal gene transfer and rooting the tree of life==
{{further|Horizontal gene transfer}}

The [[prokaryotes]] (the two domains of [[bacteria]] and [[archaea]]) and certain animals such as [[bdelloid rotifer]]s<ref>{{cite web |url=https://www.science.org/content/article/bdelloids-surviving-borrowed-dna |title=Bdelloids Surviving on Borrowed DNA |author=Watson, Traci |date=15 November 2012 |publisher=Science/AAAS News}}</ref> freely pass genetic information between unrelated organisms by [[horizontal gene transfer]]. Recombination, gene loss, duplication, and gene creation are a few of the processes by which genes can be transferred within and between bacterial and archaeal species, causing variation that is not due to vertical transfer.<ref name="pmid10097118">{{Cite journal |last1=Jain |first1=R. |last2=Rivera |first2=M. C. |last3=Lake |first3=J. A. |title=Horizontal gene transfer among genomes: the complexity hypothesis |journal=PNAS |volume=96 |issue=7 |pages=3801–6 |year=1999 |pmid=10097118 |doi=10.1073/pnas.96.7.3801 |pmc=22375 |bibcode=1999PNAS...96.3801J |doi-access=free }}</ref><ref name="Lawton">{{cite magazine |first=Graham |last=Lawton |title=Why Darwin was wrong about the tree of life |date=21 January 2009 |url=https://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?page=1 |access-date=12 Feb 2009 |magazine=[[New Scientist]] Magazine |issue= 2692}}</ref><ref>{{cite journal |last1=Doolittle |first1=W. Ford |year=2000 |title=Uprooting the tree of life |url=http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf |journal=Scientific American |volume=282 |issue=6 |pages=90–95 |url-status=dead |archive-url=https://web.archive.org/web/20060907081933/http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf |archive-date=2006-09-07 |doi=10.1038/scientificamerican0200-90 |pmid=10710791 |bibcode=2000SciAm.282b..90D }}</ref> There is emerging evidence of horizontal gene transfer within the prokaryotes at the single and multicell level, so the tree of life does not explain the full complexity of the situation in the prokaryotes.<ref name="Lawton" /> This is a major problem for the tree of life because there is consensus that eukaryotes arose from a fusion between bacteria and archaea, meaning that the tree of life is not fully bifurcating and should not be represented as such for that important node.<ref>{{Cite journal |last=Doolittle |first=W. Ford |date=1997-11-25 |title=Fun with genealogy |journal=Proceedings of the National Academy of Sciences |language=en |volume=94 |issue=24 |pages=12751–12753 |doi=10.1073/pnas.94.24.12751 |issn=0027-8424 |pmc=34172 |pmid=9398070|bibcode=1997PNAS...9412751D |doi-access=free }}</ref> Secondly, unrooted [[phylogenetic network]]s are not true evolutionary trees (or trees of life) because there is no directionality, and therefore the tree of life needs a root.<ref>{{Cite journal |last1=Iwabe |first1=N |last2=Kuma |first2=K |last3=Hasegawa |first3=M |last4=Osawa |first4=S |last5=Miyata |first5=T |date=December 1989 |title=Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. |journal=Proceedings of the National Academy of Sciences |language=en |volume=86 |issue=23 |pages=9355–9359 |doi=10.1073/pnas.86.23.9355 |pmid=2531898 |pmc=298494 |bibcode=1989PNAS...86.9355I |issn=0027-8424|doi-access=free }}</ref>

<gallery mode="packed" heights="250">
File:Circular timetree-of-life 2009.jpg|Hedges and Kumar's circular timetree of life, of 1,610 families<ref>{{Cite book |url=https://www.worldcat.org/oclc/320914412 |title=The timetree of life |date=2009 |publisher=Oxford University Press |others=S. Blair Hedges, Sudhir Kumar |isbn=978-0-19-156015-6 |location=Oxford |oclc=320914412}}</ref>
File:Spiral timetree.jpg|Hedges et al.'s 2015 spiral timetree of life of 50,632 species<ref name="Hedges 835–845"/>
File:Tree of life SVG.svg|[[David Hillis]]'s 2008 plot of the tree of life, based on completely sequenced [[genome]]s
File:A Novel Representation Of The Tree Of Life.png|A 2016 ([[Metagenomics|metagenomic]]) representation of the tree of life (unrooted) using [[ribosomal protein]] sequences<ref name="NM-20160411" />
</gallery>

==See also==
{{div col|colwidth=30}}
* [[Bacterial phyla]]
* [[Cladistics]]
* [[Common descent]]
* [[Coral of life]]
* [[Family tree]]
* [[Symbiogenesis]]
* [[TimeTree]]
* [[Tree of Life Web Project]]
{{div col end}}

==References==
{{reflist|colwidth=30em}}

==Further reading==
* {{cite book|ref=none |last=Darwin |first=Charles |author-link=Charles Darwin |year=1859 |title=On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life |edition=1st |location=London |publisher=John Murray |url=http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=1 |isbn=978-1-4353-9386-8 }}
* {{cite book|ref=none |last=Darwin |first=Charles |author-link=Charles Darwin |year=1872 |title=The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life |edition=6th |location=London |publisher=John Murray |url=http://darwin-online.org.uk/content/frameset?itemID=F391&viewtype=text&pageseq=1 |isbn=978-1-4353-9386-8 }}
* {{Cite journal|ref=none |last1=Doolittle |first1=W. F. |last2=Bapteste |first2=E. |doi=10.1073/pnas.0610699104 |title=Inaugural Article: Pattern pluralism and the Tree of Life hypothesis |journal=Proceedings of the National Academy of Sciences |volume=104 |issue=7 |pages=2043–2049 |year=2007 |pmid= 17261804|pmc=1892968|bibcode=2007PNAS..104.2043D |doi-access=free }}
* {{cite book|last=Sapp |first=Jan A. |url=https://books.google.com/books?id=d7zOviXnbSYC |title=The new foundations of evolution: on the tree of life |publisher=Oxford University Press |year=2009 |isbn=978-0-199-73438-2 |location=New York |author-link=Jan Sapp |ref=none}}

==External links==
* [http://tolweb.org/Life_on_Earth/1 Tree of Life Web Project] - explore complete phylogenetic tree interactively
* [https://opentreeoflife.github.io/ Tree of Life Evolution] Links species on Earth through a shared evolutionary history
* [https://demonstrations.wolfram.com/TheTreeOfLife/ The Tree of Life] by Garrett Neske, [[The Wolfram Demonstrations Project]]: "presents an interactive tree of life that allows you to explore the relationships between many different kinds of organisms by allowing you to select an organism and visualize the clade to which it belongs."
* [http://ucjeps.berkeley.edu/map2.html The Green Tree of Life] - [[Hyperbolic tree]] University of California/Jepson Herbaria
* [https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi NCBI's taxonomy database common tree]
* [https://www.onezoom.org/ OneZoom Tree of Life Explorer]

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[[Category:History of biology]]
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