Phylogenetic trees depict the evolutionary relationships among organisms. The relationships take the form of a tree with tips, branches, nodes, and a root.
Specifically, the tips of the tree represent extant, or living, taxa and the branches denote evolutionary changes between ancestors and descendants such as the change in the DNA sequence, or the evolution of a characteristic like feathers.
Groups that share an immediate common ancestor, sister taxa, are their closest relatives and share nodes, points where branches meet, like lizards and birds and rodents and humans. A basal node corresponds to the most recent common ancestor of all organisms in the tree.
Phylogenetic trees group organisms that are descendants of a common ancestor.
When a group contains the most recent common ancestor and all of its descendants, it is called a clade, or a monophyletic group. For instance, all living vertebrates with feathers are considered birds.
A paraphyletic group includes a common ancestral species and some of its descendants. For instance, all scaly animals with four legs are reptiles, with the exclusion of mammals and birds.
Historically, biologists also classified some organisms as polyphyletic. This abandoned designation grouped organisms that do not share an immediate common ancestor. For instance, Insectivora are toothless, insect-eating mammals.
The evolutionary relationships among organisms can be determined by comparing morphological or genetic features.
To construct accurate phylogenetic trees, scientists turned to methods such as maximum parsimony and maximum likelihood. Using maximum parsimony, one assumes the least amount of change between organisms.
Consider the arrangement of elk, salmon, and whale on a phylogenetic tree. Both the salmon and whale are marine animals. It would seem the simplest explanation is that salmon and whales are a monophyletic group.
A closer look at their anatomy, however, reveals that the whale and elk are more closely related. Placing elk and whales together assumes fewer evolutionary changes, a less complicated scenario that is the goal of maximum parsimony analysis.
An alternative approach, maximum likelihood, takes into account that not all changes are equally likely. So one can construct a phylogenetic tree based on the most likely scenario that leads to the observed organisms.
For instance, the scientists constructing the phylogenetic tree from DNA sequences might take into account that adenine is more easily replaced by guanine, than by thiamine.
Sophisticated computer algorithms aid the construction of the most parsimonious and most likely phylogenetic trees.
