The coral of life is a metaphor or a mathematical model useful to illustrate evolution of life or phylogeny at various levels of resolution, including individual organisms, populations, species and large taxonomic groups. Its use in biology resolves several practical and conceptual difficulties that are associated with the tree of life.
In biological context, the 'coral of life' as a metaphor is almost as old as the 'tree of life'. After returning from his voyage around the world, Darwin suggested in his notebooks that:
The tree of life should perhaps be called the coral of life, base of branches dead; so that passages cannot be seen
with obvious reference to branching corals whose dead colonies may form very thick deposits in the ocean (representing past life) with live animals occurring only on the top (recent life). This comment was illustrated by two simple diagrams, the first coral metaphors of evolution ever drawn in the history of biology. However, Darwin later abandoned his idea, and in the Origin of Species[2] he referred to the tree of life as the most appropriate means to summarize affinities of living organisms, thanks most likely to obvious connotations of this metaphor with religion, ancient and folk art and mythology.
Darwin’s early musing was rediscovered by several authors more than a century later,[3][4][5] graphical schemes as simple heuristics were drawn again early this century,[6] and corals were raised to the level of mathematically defined objects even more recently.[7]
Structure
The picture to the right explains the different parts of a coral. Vertical axis is time, horizontal axis may be richness, morphological diversity, some other population measure or even scaled arbitrarily. Each point x in the diagram corresponds to an individual, a population or a taxon. At point of time h, there is an equivalence partition of points into classes C. A class Cg1 is the ancestor of the entire branch above it, Cr1 is the closest common ancestor class of two segments. A segment S is defined by two classes such that there is no branching between them. On top in the middle is visualized a horizontal event, such as hybridization between members of different classes, leading to a new segment and thus to a fan coral.[7][8]
Advantages of corals as metaphors of phylogeny
Botanical trees and (many) corals share only one fundamental property, namely branching, which makes both of them suitable to illustrate evolutionary divergence. Regarding other features, corals are superior to trees as metaphors of phylogeny because:[7]
Only the uppermost sections of a coral are alive, whereas all parts of a tree, from its thinnest roots to the uppermost leaves, are living;
The coral starts its development from a small initial colony, grows upwards and ramifies later, while a tree grows from seed into two opposite directions, producing roots and the crown which may be equally large and similarly complex in shape;
The diameter of a tree continuously decreases from the trunk to the twigs, a property without phylogenetic implications, while corals may be even wider above than below, better symbolizing temporal change of taxonomic richness or population size;
Normally, tree branches never fuse whereas coral branches may exhibit anastomoses, thereby representing horizontal evolutionary events.
Advantages of corals as mathematical models of phylogeny
Zooming out from a network/tree of individuals to a coral diagram in 4 steps. See further examples in and
Trees as graph theoretical constructs are composed of vertices (nodes) representing biological entities and connecting edges (links) corresponding to relations between entities. Being a special case of branching silhouette diagrams, corals may also be defined mathematically; these are geometric shapes embedded into a two- or three-dimensional space with time as one axis and some other meaningful property, such as taxon richness, as the other (one or two). Regarding their applicability to represent phylogenies, corals and trees compare in the following way:
Trees are tools of discrete mathematics, and are therefore inappropriate to demonstrate evolutionary continuum, whereas corals as geometric shapes may very well serve this purpose;
Trees, by definition, cannot have cycles and – contrary to networks – are thus inappropriate to reflect horizontal events, such as hybridization or endosymbiosis, while fan corals allow links between branches;
Trees are computationally feasible, and remain fundamental tools in revealing phylogenetic relationships; corals can be constructed by hand based on trees and additional information from various sources in systematics, paleontology, geology etc.
There is considerable freedom in the graphical visualization of both trees and corals, although the latter may involve more artistic and heuristic elements.
When nodes of trees and networks represent individuals, so that the graphs demonstrate parent-offspring relations for asexual and sexual populations, respectively, one may zoom out so that the minor details (nodes and edges) of the diagram disappear and the discrete graph is smoothed into a coral – which is often called a “tree”, unfortunately.
Visualizing the entirety of life on earth
The 'coral of life'. Dotted or dashed horizontal lines show events such as cell fusion. The red explosion marks on the right mark major mass extinctions.
While corals may be drawn for any particular taxonomic group, e.g., “coral of plants,” the term “coral of life” specifically refers to all cellular life, viruses excluded.
The figure on the right is a first attempt to display a coral of life.[8]
The coral and the classification of life
Definition of taxa based on a coral. The red branch is monophyletic, just like the brown and red branches together. The dark and pale green segments exemplify a budding event which may only be possible at the species level.
The last, but not the least important, feature of the coral of life is that it requires a classification valid for the past and present life viewed together. To see how it is possible, we may refer again to Darwin, who warned that the system of Linnaean ranks works only thanks to our insufficient knowledge of the past life. It is due to the absence of extinct forms
and to the consequent wide gaps in the series, that we are enabled to divide the existing species into definable groups, such as genera, families, and tribes
Earlier, in the Origin of Species,[2] he commented that groups that are clearly separable at present, based on many characters, have much fewer differences for their ancient members, which are therefore closer to each other in the past than are their descendants in the present. That is, gaps observed between recent taxa paradoxically disappear when we go back to the ancestors – questioning the meaningfulness of Linnaean ranks . Consistently with this, Darwin suggested further that the natural classification system
must be, as far as possible, genealogical in arrangement, – that is, the co-descendants of the same form must be kept together in one group, apart from the co-descendants of any other form; but if the parent-forms are related, so will be their descendants, and the two groups together will form a larger group…
The system can be made genealogical if we abandon the rank system and consider coral branches as taxa, analogously to clades derived from tree representations of phylogeny. That is, every branch of the coral is a monophyletic group whose members are derived from the same equivalence class such that no other branches arise from that class.
↑ Hull, D. L. (1985) Darwinism as a historical entity: A historiographic proposal In: Kohn, D. (ed.) The Darwinian Heritage, pp: 773–812, Princeton: Princeton University Press
↑ Bredekamp, H. (2005). Darwins Korallen die führen Evolutionsdiagramme und die Tradition der Naturgeschichte. Berlin: Klaus Wagenbruch. ISBN3803151732.
↑ Gogarten, J. Peter; Townsend, Jeffrey P. (2005). "Horizontal gene transfer, genome innovation and evolution". Nature Reviews Microbiology. 3 (9): 679–687. doi:10.1038/nrmicro1204. PMID16138096.
↑ Maddison, Wayne P.; Maddison, David R. (1992). MacClade. Analysis of phylogeny and character evolution. Sunderland, MA: Sinauer. ISBN0878934901.
↑ Baum, David A.; Smith, Stancey D. (2012). Tree Thinking: An Introduction to Phylogenetic Biology. Greenwood, CO: Roberts and Co. ISBN978-1936221165.
↑ Darwin, Charles (1862). On the various contrivances by which British and foreign orchids are fertilised by insects, and on the good effects of intercrossing. London: John Murray. pp.330–331.
Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.
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.
Linnaean taxonomy can mean either of two related concepts:
The particular form of biological classification (taxonomy) set up by Carl Linnaeus, as set forth in his Systema Naturae (1735) and subsequent works. In the taxonomy of Linnaeus there are three kingdoms, divided into classes, and the classes divided into lower ranks in a hierarchical order.
A term for rank-based classification of organisms, in general. That is, taxonomy in the traditional sense of the word: rank-based scientific classification. This term is especially used as opposed to cladistic systematics, which groups organisms into clades. It is attributed to Linnaeus, although he neither invented the concept of ranked classification nor gave it its present form. In fact, it does not have an exact present form, as "Linnaean taxonomy" as such does not really exist: it is a collective (abstracting) term for what actually are several separate fields, which use similar approaches.
The theory of recapitulation, also called the biogenetic law or embryological parallelism—often expressed using Ernst Haeckel's phrase "ontogeny recapitulates phylogeny"—is a historical hypothesis that the development of the embryo of an animal, from fertilization to gestation or hatching (ontogeny), goes through stages resembling or representing successive adult stages in the evolution of the animal's remote ancestors (phylogeny). It was formulated in the 1820s by Étienne Serres based on the work of Johann Friedrich Meckel, after whom it is also known as Meckel–Serres law.
In biology, phylogenetics is the study of the evolutionary history of life using genetics, which is known as phylogenetic inference. It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology. The results are a phylogenetic tree—a diagram setting the hypothetical relationships between organisms and their evolutionary history.
Systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees. Phylogenies have two components: branching order and branch length. Phylogenetic trees of species and higher taxa are used to study the evolution of traits and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth.
A tree structure, tree diagram, or tree model is a way of representing the hierarchical nature of a structure in a graphical form. It is named a "tree structure" because the classic representation resembles a tree, although the chart is generally upside down compared to a biological tree, with the "stem" at the top and the "leaves" at the bottom.
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.
This is a list of topics in evolutionary biology.
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.
An evolutionary lineage is a temporal series of populations, organisms, cells, or genes connected by a continuous line of descent from ancestor to descendant. Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics.
In phylogenetics, a sister group or sister taxon, also called an adelphotaxon, comprises the closest relative(s) of another given unit in an evolutionary tree.
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood, parsimony, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space.
In historical linguistics, the tree model is a model of the evolution of languages analogous to the concept of a family tree, particularly a phylogenetic tree in the biological evolution of species. As with species, each language is assumed to have evolved from a single parent or "mother" language, with languages that share a common ancestor belonging to the same language family.
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).
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.
Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional method, by which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).
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.
The following outline is provided as an overview of and topical guide to evolution:
The term boundary paradox refers to the conflict between traditional, rank-based classification of life and evolutionary thinking. In the hierarchy of ranked categories it is implicitly assumed that the morphological gap is growing along with increasing ranks: two species from the same genus are more similar than other two species from different genera in the same family, these latter two species are more similar than any two species from different families of the same order, and so on. However, this requirement may only satisfy for the classification of contemporary organisms; difficulties arise if we wish to classify descendants together with their ancestors. Theoretically, such a classification necessarily involves segmentation of the spatio-temporal continuum of populations into groups with crisp boundaries. However, the problem is not only that many parent populations would separate at species level from their offspring. The truly paradoxical situation is that some between-species boundaries would necessarily coincide with between-genus boundaries, and a few between-genus boundaries with borders between families, and so on. This apparent ambiguity cannot be resolved in Linnaean systems; resolution is only possible if classification is cladistic.
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