A diagram that represents the nested hierarchy of clades within clades is known as a n

Abstract

Evolutionary, or phylogenetic, trees depict the evolution of a set 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 gene 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, as well as with the species tree, due to a variety of factors. A wide array of algorithms and computer programs are available for inferring phylogenetic trees from various types of data. While true evolutionary trees are rooted and most often binary (bifurcating), inferred trees may be unrooted or multifurcating.

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 modern day to the past.

The leaves of a tree, also called tips, 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 group of organisms at any hierarchical rank, such as a family, genus, or species. The tips of a phylogenetic tree are most commonly living, but may also represent the ends of extinct lineages or fossils.

As 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 one or many leaves. Branches connect to other branches at nodes, which represents the last 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 one connecting two nodes is called an internal branch (Figure 1).

Reading a tree from the past toward the present, a node indicates a point where an ancestral lineage (the branch below the node) split to give rise to two or more descendant lineages (the branches above the node). Branching on an evolutionary tree is also 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 us 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 ancestral lineage. In Figure 2, we could say that the tree supports monophyly of taxa C, D, and E or, put another way, C, D, and E together form a clade. Clades can be hierarchically nested within one another, as shown in Figure 2. A tree’s topology can now be defined more precisely as the set of clades that the tree contains.

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 assessment, is discussed in more 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, it is important to be aware that usage of the vocabulary is not always consistent in the literature, although the context is the same, that is, representation of the evolutionary relationships of taxa.

Abstract

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

3.4.3 Heatmap/dendrogram

The heatmap/dendrogram (Fig. 22.16) is a tool that allows an enormous amount of information to be presented in a visual form that is amenable to human interpretation. Dendrograms are trees that indicate similarities between annotation vectors. The MG-RAST heatmap/dendrogram has two dendrograms, one indicating the similarity/dissimilarity among metagenomic samples (x-axis dendrogram) and another indicating the similarity/dissimilarity among annotation categories (e.g., functional roles; the y-axis dendrogram). A distance metric is evaluated between every possible pair of sample abundance profiles. A clustering algorithm (e.g., ward-based clustering) then produces the dendrogram trees. Each square in the heatmap dendrogram represents the abundance level of a single category in a single sample. The values used to generate the heatmap/dendrogram figure can be downloaded as a table by clicking on the “download” button.

Adaptation

Phylogenetic trees have become a standard tool in the study of adaptation, and such uses are often referred to as the “comparative method.” First, it is necessary to establish that a particular “adaptation” is distributed as an apomorphy within the group in question and then, if there are multiple origins, to determine 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 adaptation. Indeed, some workers maintain that it is only possible to discuss adaptation in a historical context, i.e., based on explicit phylogenetic trees. Undoubtedly continued work in these areas will result in improved statistical tests for adaptation based on character distributions on phylogenetic trees.

Rooted versus Unrooted

Phylogenetic trees are either rooted or unrooted, depending on the research 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 ancestor 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 estimate the root of a tree using data and assumptions (Boykin et al., 2010). However, Steel (2012) discusses root location in random trees and points out that information 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 about the location of the ancestral root in unrooted trees (Steel, 2012).

9.2 Phylogenetic Trees

A phylogenetic tree or evolutionary tree is a diagrammatic representation of the evolutionary relationships among various taxa (Figure 9.1 A–D). It is a branching diagram composed of nodes and branches. The branching pattern of a tree is called the topology of the tree. The nodes represent taxonomic units, such as species (or higher taxa), populations, genes, or proteins. A branch is called an edge, and represents the time estimate of the evolutionary relationships among the taxonomic units. One branch can connect only two nodes. In a phylogenetic tree, the terminal nodes represent the operational taxonomic units (OTUs) or leaves. The OTUs are the actual objects—such as the species, populations, or gene or protein sequences—being compared, whereas the internal nodes represent hypothetical taxonomic units (HTUs). An HTU is an inferred unit and it represents the last common ancestor (LCA) to the nodes arising from this point. Descendants (taxa) that split from the same node form sister groups, and a taxon that falls outside the cladea is called an outgroup. For example, in Figure 9.1 B, T2 and T3 are sister groups, and T1 is an outgroup to T2 and T3.

Phylogenetic trees can be scaled or unscaled. In a scaled tree, the branch length is proportional to the amount of evolutionary divergence (e.g. the number of nucleotide substitutions) that has occurred along that branch. In an unscaled tree, the branch length is not proportional to the amount of evolutionary divergence, but usually the actual number is indicated somewhere on the branch.

Phylogenetic trees can be rooted (Figure 9.1 A and B) or unrooted (Figure 9.1 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 DNA or protein sequences. Obtaining a rooted tree is ideal, but most phylogenetic-tree-reconstruction algorithms produce unrooted trees.

Abstract

A phylogenetic tree is a graphical representation of the evolutionary relationships between biological entities, usually sequences or species. Relationships between entities are captured by the topology (branching order) and amount of evolutionary change (branch lengths) between nodes. The role of the root is to add direction to these relationships and clearly define ancestry. 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 use them and how to recognize them in published trees.