Tree of life (biology)

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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 organisms, both living and extinct, as described in a famous passage in Charles Darwin's On the Origin of Species (1859). [1]

Contents

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.

— Charles Darwin [2]

Tree diagrams originated in the medieval era to represent 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 Darwin in proposing 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.

History

Early natural classification

Edward Hitchcock's fold-out paleontological chart in his 1840 Elementary Geology Edward Hitchcock Paleontological Chart.jpg
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. [3] [4] 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. [5]

In 1809, Augier's more famous compatriot Jean-Baptiste Lamarck (1744–1829), who was acquainted with Augier's "Botanical Tree", [6] included a branching diagram of animal species in his Philosophie zoologique . [7] Unlike Augier, however, Lamarck did not discuss his diagram in terms of a genealogy or a tree, but instead named it a tableau ("depiction"). [8] 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. [9]

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 Palms and Man. [10]

The first edition of 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". [11] It shows a model of 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". [12]

In 1858, a year before Darwin's Origin, the paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree labelled with letters. [13] Although not a creationist, Bronn did not propose a mechanism of change. [14]

Darwin

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 a10, f10, and m10. Similarly, the descendants of I have diversified to become the new varieties w10 and z10. The process is extrapolated for a further four thousand generations so that the descendants of A and I become fourteen new species labelled a14 to z14. 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." [15] 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:

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 Ornithorhynchus or 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 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.

—  Darwin, 1859. [16]

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. [17] 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. [18] Petter Hellström has argued that Darwin consciously named his tree after the biblical Tree of Life, as described in Genesis, thus relating his theory to the religious tradition. [8]

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. [19] 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". [20] 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 "Menschen") at the top of the tree. [21]

Developments since 1990

Universal phylogenetic tree in rooted form, showing the three domains (Woese, Kandler, Wheelis 1990, p. 4578 ) PhylogeneticTree, Woese 1990.PNG
Universal phylogenetic tree in rooted form, showing the three domains (Woese, Kandler, Wheelis 1990, p. 4578 )

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 as the highest rank of classification. They suggested and formally defined the terms Bacteria, Archaea and Eukarya for the three domains of life. [22] It was the first tree founded on molecular phylogenetics and microbial evolution as its basis. [23] [24]

The model of a tree is still considered valid for eukaryotic life forms. Trees have been proposed with either four [25] [26] or two supergroups. [27] 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." [28]

In 2015, the third version of TimeTree was released, with 2,274 studies and 50,632 species, represented in a spiral tree of life, [29] 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. [30] Another database, TimeTree, helps biologists to evaluate phylogeny and divergence times. [31]

In 2016, a new tree of life (unrooted), summarising the evolution of all known life forms, was published, illustrating the latest genetic findings that the branches were mainly composed of bacteria. The new study incorporated over a thousand newly discovered bacteria and archaea. [32] [33] [34]

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). [35]

Horizontal gene transfer and rooting the tree of life

The prokaryotes (the two domains of bacteria and archaea) and certain animals such as bdelloid rotifers [36] 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. [37] [38] [39] 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. [38] 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. [40] Secondly, unrooted phylogenetic networks are not true evolutionary trees (or trees of life) because there is no directionality, and therefore the tree of life needs a root. [41]

See also

Related Research Articles

Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth.

<span class="mw-page-title-main">Clade</span> Group of a common ancestor and all descendants

In biological phylogenetics, a clade, also known as a monophyletic group or natural group, is a grouping of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. In the taxonomical literature, sometimes the Latin form cladus is used rather than the English form. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields.

<span class="mw-page-title-main">Evolution</span> Change in the heritable characteristics of biological populations

Evolution is the change in the heritable characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certain characteristics becoming more or less common within a population over successive generations. The process of evolution has given rise to biodiversity at every level of biological organisation.

In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a set of hypotheses about the relationships that reflect the evolutionary history of a group of organisms.

<span class="mw-page-title-main">Carl Woese</span> American microbiologist (1928–2012)

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois Urbana–Champaign.

<span class="mw-page-title-main">Kingdom (biology)</span> Taxonomic rank

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

<span class="mw-page-title-main">Domain (biology)</span> Taxonomic rank

In biological taxonomy, a domain, also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it 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. 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 focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

<span class="mw-page-title-main">Three-domain system</span> Hypothesis for classification of life

The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea from Bacteria as completely different organisms. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as Eukaryotes are considered as a clade of Archaea.

<span class="mw-page-title-main">Evolutionary biology</span> Study of the processes that produced the diversity of life

Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed on to their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

<span class="mw-page-title-main">Last universal common ancestor</span> Most recent common ancestor of all current life on Earth

The last universal common ancestor (LUCA) is the hypothesized common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya originated. The cell had a lipid bilayer; it possessed the genetic code and ribosomes which translated from DNA or RNA to proteins. The LUCA probably existed at latest 3.6 billion years ago, and possibly as early as 4.3 billion years ago or earlier. The nature of this point or stage of divergence remains a topic of research.

<span class="mw-page-title-main">Two-empire system</span> Biological classification system

The two-empire system was the top-level biological classification system in general use from the early 20th century until the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

<span class="mw-page-title-main">Neomura</span>

Neomura is a proposed clade of biological life composed of the two domains Archaea and Eukaryota, coined by Thomas Cavalier-Smith in 2002. Its name reflects the hypothesis that both archaea and eukaryotes evolved out of the domain Bacteria, and one of the major changes was the replacement of the bacterial peptidoglycan cell walls with other glycoproteins.

<span class="mw-page-title-main">Horizontal gene transfer in evolution</span> Evolutionary consequences of transfer of genetic material between organisms of different taxa

Horizontal gene transfer (HGT) refers to the transfer of genes between distant branches on the tree of life. In evolution, it can scramble the information needed to reconstruct the phylogeny of organisms, how they are related to one another.

<span class="mw-page-title-main">Bacterial taxonomy</span> Rank based classification of bacteria

Bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks.

Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.

The Woeseian revolution was the progression of the phylogenetic tree of life concept from two main divisions, known as the Prokarya and Eukarya, into three domains now classified as Bacteria, Archaea, and Eukaryotes. The discovery of the new domain stemmed from the work of biophysicist Carl Woese in 1977 from a principle of evolutionary biology designated as Woese's dogma. It states that the evolution of ribosomal RNA (rRNA) was a necessary precursor to the evolution of modern life forms. Although the three-domain system has been widely accepted, the initial introduction of Woese’s discovery received criticism from the scientific community.

<span class="mw-page-title-main">Reticulate evolution</span> Merging of lineages

Reticulate evolution, or network evolution is the origination of a lineage through the partial merging of two ancestor lineages, leading to relationships better described by a phylogenetic network than a bifurcating tree. Reticulate patterns can be found in the phylogenetic reconstructions of biodiversity lineages obtained by comparing the characteristics of organisms. Reticulation processes can potentially be convergent and divergent at the same time. Reticulate evolution indicates the lack of independence between two evolutionary lineages. Reticulation affects survival, fitness and speciation rates of species. 

<span class="mw-page-title-main">Timetree</span>

A timetree is a phylogenetic tree scaled to time. It shows the evolutionary relationships of a group of organisms in a temporal framework.

References

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  2. ↑ Darwin, Charles (1859). "Four: Natural Selection; or the Survival of the Fittest". On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life (First Edition, First Thousand ed.). London: John Murray. p. 129.
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  41. ↑ Iwabe, N; Kuma, K; Hasegawa, M; Osawa, S; Miyata, T (December 1989). "Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes". Proceedings of the National Academy of Sciences. 86 (23): 9355–9359. Bibcode:1989PNAS...86.9355I. doi: 10.1073/pnas.86.23.9355 . ISSN   0027-8424. PMC   298494 . PMID   2531898.
  42. ↑ The timetree of life. S. Blair Hedges, Sudhir Kumar. Oxford: Oxford University Press. 2009. ISBN   978-0-19-156015-6. OCLC   320914412.{{cite book}}: CS1 maint: others (link)

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