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Phylogenetic Trees

This document summarizes phylogenetic trees and how they are used to define evolutionary relationships between taxa like organisms, species, or genes. Phylogenetic trees are typically built using single-nucleotide polymorphisms (SNPs) between DNA sequences of different strains. More complex maximum likelihood methods incorporate evolutionary models to estimate the most likely tree given the observed SNP changes. The confidence in relationships depicted in phylogenetic trees can be assessed using bootstrapping techniques.

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85 views3 pages

Phylogenetic Trees

This document summarizes phylogenetic trees and how they are used to define evolutionary relationships between taxa like organisms, species, or genes. Phylogenetic trees are typically built using single-nucleotide polymorphisms (SNPs) between DNA sequences of different strains. More complex maximum likelihood methods incorporate evolutionary models to estimate the most likely tree given the observed SNP changes. The confidence in relationships depicted in phylogenetic trees can be assessed using bootstrapping techniques.

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Phylogenetic trees are depictions of the estimated

evolutionary relationships between taxa - these can be


organisms, species, strains or even genes.

Phylogenetic trees can be used to define relationships between


strains of bacteria. In an outbreak, this can identify very closely
related strains and reveal which bacterial strains have been
transmitted to whom. The taxa are on the tips of the trees, and
the internal nodes of the tree represent their hypothetical
ancestors. Nodes and taxa are connected by branches.
Groups of taxa that share a unique common ancestor are
considered a clade.

How are the relationships calculated?

Phylogenetic trees based on DNA sequence are typically built


using SNPs (single-nucleotide polymorphisms). The simplest
methods are based solely on the number of SNPs between
different strains. However, there are more complex methods
such as maximum likelihood, which gives the most likely tree
that explains the SNP changes shown, given a specific model of
evolution. Evolutionary models incorporate information such as
the frequency of different SNP changes (for example, the DNA
base change A to G is more common than A to C), and the rate
of evolution.

A phylogenetic tree is an estimate of the relationships between


taxa, and can be different depending on the method or
evolutionary model used. Phylogenies can also be greatly
influenced by the choice of information to include. To determine
how confident we should be in the relationships between taxa,
we can use a statistical procedure called bootstrapping. This
is where multiple (usually 100s or 1000s) alternative trees are
generated, and each node of the tree is given a value based on
the proportion of alternative trees that support it. A value of 1
means that all the bootstraps support this part of the tree. A
value of 0.5 means that only 50% the bootstraps support it.

Different types of tree

The most common way to display a tree is as


a phylogram (see Figure A and B), where the branch lengths
are variable, and represent the evolutionary distance between
the nodes.

For trees displayed in a rectangular fashion (as in Figure A),


evolutionary distances are represented by horizontal branches.
One can work out the inferred evolutionary distance between
two taxa by adding up all the horizontal branch lengths that join
them. The order and length of the vertical branches does not
mean anything – these are just organised to make the tree
readable. Trees can also be shown in a radial or star fashion
(Figure B), where all of the branches correspond to evolutionary
distances. Figure A shows a rooted rectangular tree, where the
position of the inferred common ancestor of all the bacteria is
known. To make a rootedtree, researchers usually include an
extra, distantly-related strain as an outgroup. In an outbreak, a
rooted tree can be useful as it enables us to determine the
order of infections in a transmission chain. However, for
bacterial studies an unrooted tree, with no extra outgroup
strain, is often sufficient (Figure B). It is important to remember
that phylogenetic trees that look very different can actually show
the same information, as our two examples below do.
Figure (A) rooted and (B) unrooted phylogenetic trees, with
key features shown. (Click image to expand)

Now look at the trees in Figure A and B in more detail. As we


know, they both show the same information, but tree A
is rooted by adding a distantly related strain. The node
separating bacterial strains 1 and 2 from strains 3, 4 and 5 is
the most confident relationship in the tree with 100% bootstrap
support. The most closely related two strains are bacteria 3 and
bacteria 4, as shown by branch length in both the horizontal
tree (A) and the radial tree (B). The least confident relationship
in the tree is bacteria 1 and bacteria 2, which has 70%
bootstrap support. This means that the closest relative of each
of these bacteria might actually be a different isolate, elsewhere
in the tree. Including more bacteria in the phylogeny would
make these relationships clearer - this is why bacterial
phylogenies in research often include hundreds or even
thousands of strains.

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