Phylogenetic tree

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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. [1] [2] 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 (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. [1] [2]

Contents

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, [3] 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

The idea of a 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 evolutionary "tree" in his 1859 book On the Origin of Species . Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages.

The term phylogenetic, or phylogeny, derives from the two ancient greek words φῦλον (phûlon), meaning "race, lineage", and γένεσις (génesis), meaning "origin, source". [4] [5]

Properties

Rooted tree

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. Phylogenetic treePureThickBraille.jpg
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 (see two graphics at top) is a directed tree with a unique node — the root — corresponding to the (usually imputed) most recent common ancestor of all the entities at the 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 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).

The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup. Another method is midpoint rooting, or a tree can also be rooted by using a non-stationary substitution model. [6]

Unrooted tree

An unrooted phylogenetic tree for myosin, a superfamily of proteins MyosinUnrootedTree.jpg
An unrooted phylogenetic tree for myosin, a superfamily of proteins

Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. [8] Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis. [9]

Bifurcating versus multifurcating

Both rooted and unrooted trees can be either 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.

Labeled versus unlabeled

Both rooted and unrooted trees can be either labeled or unlabeled. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. Some sequence-based trees built from a small genomic locus, such as Phylotree, [10] feature internal nodes labeled with inferred ancestral haplotypes.

Enumerating trees

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. Number of trees as a function of the number of leaves.svg
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.

The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more labeled than unlabeled trees, more multifurcating than bifurcating trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For bifurcating labeled trees, the total number of rooted trees is:

for , represents the number of leaf nodes. [11]

For bifurcating labeled trees, the total number of unrooted trees is: [11]

for .

Among labeled bifurcating trees, the number of unrooted trees with leaves is equal to the number of rooted trees with leaves. [2]

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

Counting trees. [11]
Labeled
leaves		Binary
unrooted trees		Binary
rooted trees		Multifurcating
rooted trees		All possible
rooted trees
11101
21101
31314
43151126
515105131236
61059451,8072,752
794510,39528,81339,208
810,395135,135524,897660,032
9135,1352,027,02510,791,88712,818,912
102,027,02534,459,425247,678,399282,137,824

Special tree types

Dendrogram of the phylogeny of some dog breeds Phylogenetic tree of dogs.png
Dendrogram of the phylogeny of some dog breeds

Dendrogram

A dendrogram is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree. [12]

Cladogram

A cladogram only represents a branching pattern; i.e., its branch lengths do not represent time or relative amount of character change, and its internal nodes do not represent ancestors. [13]

A chronogram of Lepidoptera. In this phylogenetic tree type, branch lengths are proportional to geological time. Phylogenetic chart of Lepidoptera chronogram.svg
A chronogram of Lepidoptera. In this phylogenetic tree type, branch lengths are proportional to geological time.

Phylogram

A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change. [15]

A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths. [16]

Dahlgrenogram

A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree.

Phylogenetic network

A phylogenetic network is not strictly speaking a tree, but rather a more general graph, or a directed acyclic graph in the case of rooted networks. They are used to overcome some of the limitations inherent to trees.

Spindle diagram

A spindle diagram, showing the evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are often used in evolutionary taxonomy. Spindle diagram.jpg
A spindle diagram, showing the evolution of the vertebrates 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. [17] It represents taxonomic diversity (horizontal width) against geological time (vertical axis) in order to reflect the variation of abundance of various taxa through time. However, a spindle diagram is not an evolutionary tree: [18] the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon [17] and have the disadvantage of involving the paraphyly of the parental group. [19] This type of diagram is no longer used in the form originally proposed. [19]

Coral of life

The Coral of Life The Coral Of Life Prototype.svg
The Coral of Life

Darwin [20] also mentioned that the coral may be a more suitable metaphor than the tree. Indeed, phylogenetic corals are useful for portraying past and present life, and they have some advantages over trees (anastomoses allowed, etc.). [19]

Construction

Phylogenetic trees composed with a nontrivial number of input sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic distance from multiple sequence alignments, 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 framework, and apply an explicit model of evolution to phylogenetic tree estimation. [2] Identifying the optimal tree using many of these techniques is NP-hard, [2] so heuristic search and 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: [21]

Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using T-theory. [22]

File formats

Trees can be encoded in a number of different formats, all of which must represent the nested structure of a tree. They may or may not encode branch lengths and other features. Standardized formats are critical for distributing and sharing trees without relying on graphics output that is hard to import into existing software. Commonly used formats are

Limitations of phylogenetic analysis

Although phylogenetic trees produced on the basis of sequenced genes or 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 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 noisy; [23] the analysis can be confounded by genetic recombination, [24] horizontal gene transfer, [25] hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences.

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 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), [26] or genes that would be expected to evolve under different selective regimes, so that homoplasy (false homology) would be unlikely to result from natural selection.

When extinct species are included as terminal nodes 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 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 networks are used when bifurcating trees are not suitable, due to these complications which suggest a more reticulate evolutionary history of the organisms sampled.

See also

Related Research Articles

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 hypothesis of relationships that reflects the evolutionary history of a group of organisms.

<span class="mw-page-title-main">Cladogram</span> Diagram used to show relations among groups of organisms with common origins

A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.

<span class="mw-page-title-main">Outgroup (cladistics)</span>

In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.

In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy. In other words, under this criterion, the shortest possible tree that explains the data is considered best. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.

<span class="mw-page-title-main">Substitution model</span> Description of the process by which states in sequences change into each other and back

In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules represented as sequence of symbols. Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances are typically calculated using substitution models. Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree.

<span class="mw-page-title-main">Polytomy</span> Multifurcated node of a phylogenetic tree

An internal node of a phylogenetic tree is described as a polytomy or multifurcation if (i) it is in a rooted tree and is linked to three or more child subtrees or (ii) it is in an unrooted tree and is attached to four or more branches. A tree that contains any multifurcations can be described as a multifurcating 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.

Perfect phylogeny is a term used in computational phylogenetics to denote a phylogenetic tree in which all internal nodes may be labeled such that all characters evolve down the tree without homoplasy. That is, characteristics do not hold to evolutionary convergence, and do not have analogous structures. Statistically, this can be represented as an ancestor having state "0" in all characteristics where 0 represents a lack of that characteristic. Each of these characteristics changes from 0 to 1 exactly once and never reverts to state 0. It is rare that actual data adheres to the concept of perfect phylogeny.

Ancestral reconstruction is the extrapolation back in time from measured characteristics of individuals, populations, or specie to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence, the amino acid sequence of a protein, the composition of a genome, a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species. This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the evolutionary history of the species in the tree. Since modern genetic sequences are essentially a variation of ancient ones, access to ancient sequences may identify other variations and organisms which could have arisen from those sequences. In addition to genetic sequences, one might attempt to track the changing of one character trait to another, such as fins turning to legs.

Tree rearrangements are deterministic algorithms devoted to search for optimal phylogenetic tree structure. They can be applied to any set of data that are naturally arranged into a tree, but have most applications in computational phylogenetics, especially in maximum parsimony and maximum likelihood searches of phylogenetic trees, which seek to identify one among many possible trees that best explains the evolutionary history of a particular gene or species.

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 comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent. This realization inspired the development of explicitly phylogenetic comparative methods. Initially, these methods were primarily developed to control for phylogenetic history when testing for adaptation; however, in recent years the use of the term has broadened to include any use of phylogenies in statistical tests. Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.

Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree. The distance matrix can come from a number of different sources, including measured distance or morphometric analysis, various pairwise distance formulae applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data. For phylogenetic character data, raw distance values can be calculated by simply counting the number of pairwise differences in character states.

<span class="mw-page-title-main">Unrooted binary tree</span>

In mathematics and computer science, an unrooted binary tree is an unrooted tree in which each vertex has either one or three neighbors.

<span class="mw-page-title-main">Hydrobacteria</span> Clade of bacteria

Hydrobacteria is a taxon containing approximately one-third of prokaryote species, mostly gram-negative bacteria and their relatives. It was found to be the closest relative of an even larger group of Bacteria, Terrabacteria, which are mostly gram positive bacteria. The name Hydrobacteria refers to the moist environment inferred for the common ancestor of those species. In contrast, species of Terrabacteria possess adaptations for life on land.

Horizontal or lateral gene transfer is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate investigations of the evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages.

Multispecies Coalescent Process is a stochastic process model that describes the genealogical relationships for a sample of DNA sequences taken from several species. It represents the application of coalescent theory to the case of multiple species. The multispecies coalescent results in cases where the relationships among species for an individual gene can differ from the broader history of the species. It has important implications for the theory and practice of phylogenetics and for understanding genome evolution.

<span class="mw-page-title-main">Phylogenetic reconciliation</span> Technique in evolutionary study

In phylogenetics, reconciliation is an approach to connect the history of two or more coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree representing the evolution of an entity can be drawn within another phylogenetic tree representing an encompassing entity to reveal their interdependence and the evolutionary events that have marked their shared history. The development of reconciliation approaches started in the 1980s, mainly to depict the coevolution of a gene and a genome, and of a host and a symbiont, which can be mutualist, commensalist or parasitic. It has also been used for example to detect horizontal gene transfer, or understand the dynamics of genome evolution.

References

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  2. 1 2 3 4 5 Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
  3. ↑ Kinene, T.; Wainaina, J.; Maina, S.; Boykin, L. (21 April 2016). "Rooting Trees, Methods for". Encyclopedia of Evolutionary Biology: 489–493. doi:10.1016/B978-0-12-800049-6.00215-8. ISBN   9780128004265. PMC   7149615 .
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