Phylogenetic Tree
A phylogenetic tree is a diagram that visualizes the evolutionary relationships between different
organisms or groups of organisms, often species. It depicts how these taxa are related through a
common ancestor, forming a branching pattern that reflects their evolutionary history
Purposes: Phylogenetic trees help us understand the evolutionary history, relatedness, and
diversification of organisms. They provide insights into the patterns of evolutionary change and can
be used to study various biological phenomena.
Branches:
These represent lineages that evolve over time and connect different taxa.
Nodes:
These represent the points where lineages diverge, indicating a common ancestor.
Root:
The base of the tree, representing the most recent common ancestor of all taxa included in the
tree.
Tips (or leaves):
These represent the individual taxa (species, genes, etc.) at the end of the branches.
Outgroup:
A taxon outside the group of interest, used as a reference point to root the tree.
Phylogenetic trees are constructed using various methods, such as maximum likelihood, maximum
parsimony, or distance-based algorithms. These methods analyze genetic or morphological data to
infer evolutionary relationships.
Branch lengths in a phylogenetic tree can represent different factors, such as genetic distance, time,
or evolutionary change. Longer branches typically indicate more divergence or greater genetic
differences between taxa.
Phylogenetic trees are based on available data and assumptions, so they can be affected by data
quality, incomplete sampling, or inaccuracies in the underlying models. Additionally, the
interpretation of tree topologies can sometimes be challenging due to complex evolutionary
processes.
Plant phylogenetic tree
This tree illustrates the evolutionary relationships among major plant groups.
It showcases the divergence of plant lineages from a common ancestor and the subsequent
evolution of mosses, ferns, gymnosperms, and angiosperms (flowering plants).
The tree highlights the relationships between different plant groups based on shared derived
traits and genetic information.
Human phylogenetic tree
Humans, several non-human primates, and four classic model organisms used in aging
research are depicted on a phylogenetic tree.
The horizontal axis represents the number of millions of years since the divergence of two
species. The divergence between humans and marmosets is estimated to have occurred
approximately 42,6 million years ago. The divergence between humans and fruit flies occurred
roughly 782 million years ago.
Terminology of phylogenetic trees
Taxon: A taxon is any group of organisms classified at a specific level, such as a species,
genus, family, order, or higher taxonomic ranks.
Node: A node, also known as a vertex, is the intersection of branches in a phylogenetic tree. It
represents an ancestor from whom two or more descendant lineages diverged.
Root: A phylogenetic tree’s root represents the most recent common ancestor of all taxa
included in the tree. It is typically depicted at the tree’s base or beginning.
Branch: A branch is an evolutionary lineage that connects a node to a tip or another node. It
represents the course of evolution or diversification.
Clade: A clade is a monophyletic group within a phylogenetic tree consisting of an ancestor
and all of its descendants. It denotes a distinct evolutionary lineage and is characterized by a
common ancestor.
Tip/Leaf: A tip, also known as a leaf or terminal node, represents a taxon or group of
organisms that are extant or presently living at the end of a branch. The tips of a taxonomic tree
may correspond to individual species or larger taxonomic categories.
Branch Length: The length of a branch represents the quantity of evolutionary change that has
occurred along that branch. It can be measured in terms of time (for instance, millions of years)
or genetic or morphological differences (for instance, DNA substitutions).
Phylogenetic Distance: The measure of evolutionary difference or similarity between two taxa
or groups. It is typically estimated using genetic or morphological data and can be quantified
using a variety of techniques, such as genetic distances or character-based measures.
Homology: Homology refers to the similarity between characteristics or traits of various
organisms owing to a common ancestor. Homologous characteristics are inherited from a
common ancestor and may have changed or diverged over time.
Homoplasy: Homoplasy refers to the similarity between characteristics or traits in various
organisms that is not due to a common ancestor but rather arises independently. Homoplastic
characteristics may be the result of convergent evolution, parallel evolution, or evolutionary
reversals.
Bootstrap Support: Bootstrap support is a statistical confidence measure for a phylogenetic
tree’s branching pattern. It is determined by repeatedly resampling the original dataset and
evaluating the stability of the inferred relationships.
