Biology · Introductory biology · Concept
Phylogenetic trees: reading relatedness
A phylogenetic tree is a hypothesis about how organisms are related through common ancestry. Its tips are the taxa compared; each node is a common ancestor; and a clade is an ancestor with all of its descendants. Two taxa are more closely related when they share a more recent common ancestor, whatever their order along the tips. Trees are built from shared derived characters, and parsimony prefers the tree that needs the fewest evolutionary changes.
Reading a tree
Read relatedness from the branching, not from the order of the tips: a node can turn like a mobile without changing the tree. Two taxa joined at a node near the tips share a recent common ancestor; taxa joined only near the root are distant relatives. The root is the ancestor of everything on the tree, and the tips are the organisms being compared, not one another’s ancestors.
| Taxon | Four limbs | Amniotic egg | Hair |
|---|---|---|---|
| Shark | No | No | No |
| Frog | Yes | No | No |
| Lizard | Yes | Yes | No |
| Mouse | Yes | Yes | Yes |
| Human | Yes | Yes | Yes |
Clades
A clade, or monophyletic group, is an ancestor and all of its descendants; one cut below its node removes it from the tree. A group that leaves out some descendants, such as reptiles without birds, is paraphyletic and is not a clade. Two taxa that are each other’s closest relatives on a tree are sister taxa.
Building a tree from characters
A shared derived character, a trait that arose in a common ancestor and was passed to its descendants, marks a clade: hair and milk mark the mammals. A character every taxon shares says nothing about grouping within the tree. An outgroup, a taxon outside the group being studied, shows which state of a character is ancestral.
Parsimony
Different trees can fit the same data. Parsimony chooses the tree that needs the fewest changes in its characters, on the reasoning that a shared complex trait is more likely inherited once than evolved twice. Similar traits that evolved separately, such as the wings of bats and birds, are homoplasy, and they can mislead.
Common mistakes
- Reading relatedness from the order of the tips: neighbors along the tips can be distant relatives; follow the branches back to their most recent common ancestor.
- Treating one living species as the ancestor of another: the tips are present-day or sampled taxa; ancestors sit at the nodes.
- Calling any group of similar organisms a clade: a clade must hold an ancestor and all of its descendants.
- Counting characters every taxon shares as evidence of grouping: only shared derived characters mark clades.
Key terms
- Phylogeny
- The evolutionary history of a group, drawn as a tree. Branch points are common ancestors; the order of the tips down the side means nothing.
- Taxon
- Any named group of organisms, such as a species, a genus or a family. On a tree, each tip is a taxon.
- Clade
- An ancestor and all of its descendants: a group you can cut off a tree with one snip.
- Most recent common ancestor
- The most recent common ancestor of two taxa: the node where their branches meet. The more recent it is, the more closely they are related.
- Sister taxa
- Two taxa that share a most recent common ancestor with no other taxon on the tree, so each is the other’s closest relative there.
- Tree topology
- The branching pattern of a tree. Rotating branches around a node leaves it unchanged; only how the branches connect shows relationships.
- Polytomy
- A node with more than two branches, usually meaning the order of those splits is not yet known.
- Derived character
- A trait changed from the ancestral state, such as hair in mammals. A derived trait shared by a group (a synapomorphy) is evidence that the group is a clade.
- Outgroup
- A taxon outside the group being studied, used to decide which character states are ancestral. A state the outgroup shares is taken as ancestral; a state found only inside the group, as derived.
- Homology
- Similarity inherited from a common ancestor, such as the same bones in a human arm and a bat’s wing.
- Homoplasy
- Similarity that evolved independently rather than from a shared ancestor, such as the wings of birds and bats. It can mislead the building of a tree.
- Phylogenetic parsimony
- Choosing the tree that needs the fewest changes in its characters. A tree’s parsimony score counts those changes; the lowest score wins.
- Character matrix
- A table of taxa against characters, giving each taxon’s state for each trait (present or absent, or a letter): the data a parsimony tree is built from.
Work through an example
A tree of five animals reads, in Newick form, (Shark,(Frog,(Lizard,(Mouse,Human)))). Which animals are the lizard’s closest relatives? Do the frog and the lizard form a clade? Using the characters four limbs, amniotic egg and hair, how many changes does the tree need?
Find the closest relatives on a tree →Sources and scope
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