Phylogenetic Tree

To generate phylogenetic trees, a triangle matrix is generated from inferred Deoxyribonucleic acid distances of all or a subset of the possible combinations of heteroduplex pairings.

From: PCR Strategies , 1995

Evolutionary Trees

Fifty. Nakhleh , in Brenner's Encyclopedia of Genetics (2d Edition), 2013

Abstract

Evolutionary, or phylogenetic, trees depict the development of a prepare of taxa from their most recent common ancestor (MRCA). A species tree is a phylogenetic tree that models the evolutionary history of a set of species (or populations). A factor tree is a phylogenetic tree that models a genealogy of a gene. Gene trees of different genes sampled from a set of species may disagree with each other, likewise equally with the species tree, due to a variety of factors. A wide array of algorithms and estimator programs are available for inferring phylogenetic copse from various types of data. While true evolutionary trees are rooted and most ofttimes binary (bifurcating), inferred trees may exist unrooted or multifurcating.

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Phylogenetic Tree

A.D. Scott , D.A. Baum , in Encyclopedia of Evolutionary Biology, 2016

Tree Terminology

Phylogenetic trees, by analogy to botanical trees, are made of leaves, nodes, and branches ( Figure 1). Let us consider a tree from the canopy down to the trunk, or from the mod 24-hour interval to the by.

Figure 1. Components of a phylogenetic tree.

The leaves of a tree, also called tips, tin can be species, populations, individuals, or even genes. If the tips represent a formally named group, they are called taxa (singular: taxon). A 'taxon' is a grouping of organisms at any hierarchical rank, such as a family, genus, or species. The tips of a phylogenetic tree are near usually living, simply may also represent the ends of extinct lineages or fossils.

Equally in the trees you are already familiar with, tips or leaves are subtended by branches. A branch, which represents the persistence of a lineage through time, may subtend 1 or many leaves. Branches connect to other branches at nodes, which represents the terminal common ancestors of organisms at the tips of the descendant lineages. A branch connecting a tip to a node is called an external branch, whereas i connecting 2 nodes is called an internal branch (Figure ane).

Reading a tree from the past toward the present, a node indicates a betoken where an ancestral lineage (the branch below the node) split to give rise to two or more than descendant lineages (the branches higher up the node). Branching on an evolutionary tree is likewise called 'cladogenesis' or 'lineage splitting.' After a lineage splits into two, evolution happens independently in these newly formed descendant lineages. The sequence of lineage splits in a tree creates its structure or 'topology.' Tree topology shows the states the branching of lineages through time that gave rise to the tips.

'Clades' are groupings on a tree that include a node and all of the lineages descended from that node. The set of all the tips in a clade is defined as being 'monophyletic,' referring to the fact that it includes all the descendants of an bequeathed lineage. In Figure ii, we could say that the tree supports monophyly of taxa C, D, and East or, put another way, C, D, and E together form a clade. Clades can be hierarchically nested within i some other, as shown in Effigy two. A tree'south topology tin now be defined more precisely as the set of clades that the tree contains.

Effigy two. Clades are highlighted in a phylogenetic tree. Note clades can be hierarchically nested.

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Fundamentals of Molecular Evolution*

Supratim Choudhuri , in Bioinformatics for Beginners, 2014

2.7.3 Phylogenetic Tree

A phylogenetic tree or evolutionary tree is a diagrammatic representation of the evolutionary relationship among various taxa. The phylogenetic tree, including its reconstruction and reliability cess, is discussed in more than detail in Chapter 9. The terms evolutionary tree, phylogenetic tree, and cladogram are often used interchangeably to mean the same thing—that is, the evolutionary relationships among taxa. The term dendrogram is also used interchangeably with cladogram, although there are subtle differences, discussed in Chapter 9. Thus, information technology is important to be aware that usage of the vocabulary is not always consistent in the literature, although the context is the aforementioned, that is, representation of the evolutionary relationships of taxa.

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Phylogenetic Tree Distances

1000. Weyenberg , R. Yoshida , in Encyclopedia of Evolutionary Biology, 2016

Abstruse

Phylogenetic trees are mathematical objects which summarize the about recent common ancestor relationships betwixt a given set of organisms. There is often a need to quantify the caste of similarity or discordance between 2 proposed trees. For instance, a person may exist interested in knowing whether the phylogenetic trees reconstructed from two distinct sequence alignments are truly different, or if the differences are and so minor every bit to be owing only to statistical variation. In this commodity we summarize several of the virtually widely known methods for defining distances betwixt phylogenetic trees, and provide examples of the calculations when feasible.

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Microbial Metagenomics, Metatranscriptomics, and Metaproteomics

Andreas Wilke , ... Folker Meyer , in Methods in Enzymology, 2013

3.4.3 Heatmap/dendrogram

The heatmap/dendrogram (Fig. 22.sixteen) is a tool that allows an enormous corporeality of information to be presented in a visual grade that is acquiescent to man interpretation. Dendrograms are copse that indicate similarities betwixt annotation vectors. The MG-RAST heatmap/dendrogram has two dendrograms, one indicating the similarity/dissimilarity amidst metagenomic samples (ten-axis dendrogram) and another indicating the similarity/dissimilarity amidst annotation categories (e.one thousand., functional roles; the y-axis dendrogram). A distance metric is evaluated betwixt every possible pair of sample affluence profiles. A clustering algorithm (eastward.g., ward-based clustering) and so produces the dendrogram copse. Each foursquare in the heatmap dendrogram represents the abundance level of a single category in a single sample. The values used to generate the heatmap/dendrogram effigy tin be downloaded as a table by clicking on the "download" button.

Effigy 22.16. Heatmap/dendrogram example in MG-RAST. The MG-RAST heatmap/dendrogram has two dendrograms, one indicating the similarity/contrast among metagenomic samples (ten-axis dendrogram) and another to indicate the similarity/dissimilarity among notation categories (due east.g., functional roles; the y-axis dendrogram).

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Phylogeny

Kevin C. Nixon , in Encyclopedia of Biodiversity (2d Edition), 2001

Accommodation

Phylogenetic copse have become a standard tool in the study of adaptation, and such uses are often referred to equally the "comparative method." Commencement, it is necessary to establish that a particular "adaptation" is distributed equally an apomorphy within the group in question and and so, if there are multiple origins, to make up one's mind if these origins are correlated with other characters and/or environmental variables. While numerous statistical approaches have been suggested for such studies, they all assume that multiple independent origins of characters correlated with environmental or historical factors are evidence of accommodation. Indeed, some workers maintain that it is only possible to hash out adaptation in a historical context, i.e., based on explicit phylogenetic trees. Undoubtedly continued work in these areas will event in improved statistical tests for adaptation based on character distributions on phylogenetic trees.

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Rooting Trees, Methods for

T. Kinene , ... L.Grand. Boykin , in Encyclopedia of Evolutionary Biology, 2016

Rooted versus Unrooted

Phylogenetic copse are either rooted or unrooted, depending on the enquiry questions being addressed. The root of the phylogenetic tree is inferred to be the oldest point in the tree and corresponds to the theoretical last common antecedent of all taxonomic units included in the tree. The root gives directionality to evolution within the tree ( Baldauf, 2003). Accurate rooting of a phylogenetic tree is important for directionality of evolution and increases the power of interpreting genetic changes between sequences (Pearson et al., 2013).

Many techniques such as molecular clock, Bayesian molecular clock, outgroup rooting, or midpoint rooting methods tend to approximate the root of a tree using information and assumptions (Boykin et al., 2010). However, Steel (2012) discusses root location in random copse and points out that data in the prior distribution of the topology alone can convey the location of the root of the tree. These results show that the tree models that treat all taxa equally and are sampling consistently convey information nigh the location of the ancestral root in unrooted trees (Steel, 2012).

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Phylogenetic Assay*

Supratim Choudhuri , in Bioinformatics for Beginners, 2014

9.2 Phylogenetic Copse

A phylogenetic tree or evolutionary tree is a diagrammatic representation of the evolutionary relationships among various taxa ( Figure nine.i A–D). It is a branching diagram composed of nodes and branches. The branching blueprint of a tree is called the topology of the tree. The nodes represent taxonomic units, such every bit species (or college taxa), populations, genes, or proteins. A branch is called an edge, and represents the time judge of the evolutionary relationships among the taxonomic units. One branch can connect but two nodes. In a phylogenetic tree, the final nodes correspond the operational taxonomic units (OTUs) or leaves. The OTUs are the bodily objects—such equally the species, populations, or gene or poly peptide sequences—being compared, whereas the internal nodes represent hypothetical taxonomic units (HTUs). An HTU is an inferred unit and it represents the final common ancestor (LCA) to the nodes arising from this betoken. Descendants (taxa) that carve up from the same node form sister groups, and a taxon that falls outside the clade a is called an outgroup. For example, in Figure ix.1 B, T2 and Tiii are sister groups, and Ti is an outgroup to Ttwo and T3.

Figure ix.ane. Dissimilar forms of presentation of the phylogenetic tree.

The phylogenetic tree in D is a dendrogram derived from hierarchical clustering (meet text). A, B, and D bear witness rooted copse, while C shows an unrooted tree. Taxa that share specific derived characters are grouped into clades. (A) Smaller clades located within a larger clade are chosen nested clades. (B) The final nodes represent the operational taxonomic units, also called "leaves"; each final node could be a taxon (species or higher taxa), or a gene or protein sequence. The internal nodes represent hypothetical taxonomic units. An HTU represents the last common ancestor to the nodes arising from this bespeak. 2 descendants that split from the aforementioned node are called sister groups and a taxon that falls outside the clade is chosen an outgroup. Rooted copse have a node from which the remainder of the tree diverges, frequently called the last universal common ancestor (LUCA).

Phylogenetic trees tin be scaled or unscaled. In a scaled tree, the co-operative length is proportional to the amount of evolutionary departure (east.thou. the number of nucleotide substitutions) that has occurred along that branch. In an unscaled tree, the co-operative length is not proportional to the amount of evolutionary divergence, but usually the actual number is indicated somewhere on the branch.

Phylogenetic copse tin exist rooted (Figure ix.ane A and B) or unrooted (Figure nine.i C). A rooted tree has a node (the root) from which the rest of the tree diverges. This root is frequently referred to as the last universal common ancestor (LUCA), from which the other taxonomic groups have descended and diverged over time. In molecular phylogenetics, the LUCA and LCA are represented by Deoxyribonucleic acid or protein sequences. Obtaining a rooted tree is platonic, only most phylogenetic-tree-reconstruction algorithms produce unrooted trees.

ix.2.one Phylogenetic Copse, Phylograms, Cladograms, and Dendrograms

In the context of molecular phylogenetics, the expressions phylogenetic tree, phylogram, cladogram, and dendrogram are used interchangeably to mean the same thing—that is, a branching tree structure that represents the evolutionary relationships amid the taxa (OTUs), which are gene/poly peptide sequences. In the traditional evolutionary sense, the OTUs in the phylogenetic tree are represented past species. A phylogram is a scaled phylogenetic tree in which the branch lengths are proportional to the amount of evolutionary divergence. For example, a branch length may be adamant past the number of nucleotide substitutions that have occurred between the continued branch points. A cladogram is a branching hierarchical tree that shows the relationships betwixt clades; cladograms are unscaled. The give-and-take dendrogram means a hierarchical cluster organisation where like objects (based on some defined criteria) are grouped into clusters; hence, a dendrogram shows the relationships amongst various clusters (Figure 9.i D). Dendrograms are also used outside the scope of phylogenetics and even exterior of biology. Dendrograms are fequently used in computational molecular biology to illustrate the branching based on clustering of genes or proteins.

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Fractalkine

Violetta Zujovic , ... T.J. Schall , in The Cytokine Handbook (Quaternary Edition), 2003

Dendrograms depicting evolutionary relationships in the growing array of chemokines and their receptors are beginning to resemble elegant Mandlebrot patterns - those eerily beautiful, iterative and self-referential tracings that have been used to draw the geometry of everything from cauliflowers to continents. Thus, it seems plumbing equipment to invoke such a complex metaphor to describe the latest layer in the baroque system decision-making leukocyte trafficking, inflammation and infectious processes. 'Fractalkine' therefore seems an appropriate name for a novel grade of chemokine that adds a new twist to models of cellular trafficking and immune regulation.

Immunology Today

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Phylogenetic Tree Rooting

Richard J. Edwards , in Encyclopedia of Bioinformatics and Computational Biology, 2019

Abstract

A phylogenetic tree is a graphical representation of the evolutionary relationships between biological entities, usually sequences or species. Relationships between entities are captured past the topology (branching lodge) and amount of evolutionary modify (branch lengths) betwixt nodes. The function of the root is to add management to these relationships and clearly define beginnings. This chapter will discuss if, when and why a phylogenetic tree should be rooted. Common rooting methods (midpoint and outgroup rooting) are introduced with comments on when to apply them and how to recognize them in published copse.

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