Phylogeny & common ancestry

Evidence that all life shares an ancestor

Every living cell stores its genes in DNA, uses almost the same genetic code to read them, builds proteins on ribosomes and breaks down glucose by glycolysis. There's no reason all life would have to work this way, so the simplest explanation is that all of it inherited these features from one ancient ancestor, often called LUCA, the last universal common ancestor.

Bodies carry evidence too. A human arm, a whale's flipper, a bat's wing and a cat's leg do very different jobs, yet they're built from the same set of bones in the same arrangement. Features that are similar because they were inherited from a common ancestor are called homologous structures. Some homologous structures are vestigial: reduced remnants with little or no function, like the small leg bones buried inside the bodies of some whales.

Reading a phylogenetic tree

A phylogenetic tree is a diagram of how groups of organisms are thought to be related. It's a hypothesis, based on the best evidence available, and it can change as new evidence comes in. A tree drawn from shared characters, often without meaningful branch lengths, is called a cladogram.

• The root is the common ancestor of everything on the tree.
• Each node (branch point) is a common ancestor that split into two lineages. Speciation events are the nodes.
• The tips are the groups being compared, usually living species.
• Two lineages that come from the same node are sister taxa: each is the other's closest relative on the tree.

To find the most recent common ancestor of two species, trace each of their branches back towards the root until they meet. The node where they join is their most recent common ancestor. The more recent that node (the closer it is to the tips), the more closely related the two species are.

Homology versus analogy

Looking alike isn't the same as being related. Analogous structures are similar because they do the same job, not because they were inherited from a common ancestor. They're the result of convergent evolution: unrelated lineages facing similar challenges and evolving similar solutions. Sharks and dolphins both have streamlined bodies and fins, but a shark is a fish and a dolphin is a mammal whose ancestors lived on land.

A good rule is that the more complex and detailed a similarity is, the more likely it reflects common ancestry. A simple streamlined shape is easy to evolve twice; an identical arrangement of dozens of bones is not.

Building a cladogram

Not every shared feature helps. A shared ancestral character is one inherited from an ancestor further back, so it's shared by everything in the group and can't separate them. A backbone is shared by all vertebrates, so it can't tell you whether a lizard is closer to a frog or a mouse. A shared derived character is a newer feature that only some members have. The amniotic egg is shared by reptiles, birds and mammals but not frogs, so it marks those groups as one branch.

Whether a character is ancestral or derived depends on which part of the tree you're looking at. To decide, you use an outgroup: a species known to have branched off before all the others. Anything the outgroup has is probably ancestral.

1. 1Make a table of which species have which characters. Include an outgroup.
2. 2Find the character shared by the most species (apart from the outgroup). It marks the first branch point.
3. 3Put the species with that character on one side of the node and those without it on the other.
4. 4Repeat with the next most widely shared character, nesting groups inside groups.
5. 5If the characters conflict, choose the tree that needs the fewest changes. This is the principle of maximum parsimony.

Every branch of a good tree forms a clade, or monophyletic group: an ancestor and all of its descendants. A group that includes an ancestor but leaves out some of its descendants is paraphyletic. The traditional "reptiles" are paraphyletic, because birds evolved from within the reptile branch but are left out of the group.

Molecular evidence

Today most trees are built from DNA, RNA or protein sequences. The logic is the same: species that share a more recent ancestor have had less time to build up differences, so their sequences are more alike. Molecular data can reveal relationships that bodies hide, as Woese's ribosomal RNA did. It works best combined with anatomical evidence, since sequences can also match by chance.

If a gene collects mutations at a fairly steady rate, the number of differences can estimate how long ago two lineages split. This is a molecular clock. It has to be calibrated with dated fossils, and the rate can differ between genes and lineages, so its dates come with error bars.

Key terms

Phylogenetic tree / cladogram

A diagram of hypothesised evolutionary relationships / one built from shared derived characters.

Node

A branch point on a tree, representing a common ancestor that split into two lineages.

Sister taxa

Two lineages that come from the same node; each other's closest relatives on the tree.

Homologous / analogous structures

Similar because inherited from a common ancestor / similar because of convergent evolution.

Shared derived character

A newer feature found in some members of a group, used to define a branch.

Outgroup

A species that branched off before the group being studied, used to tell ancestral from derived characters.

Monophyletic / paraphyletic group

An ancestor and all its descendants / an ancestor and only some of its descendants.

Maximum parsimony

Choosing the tree that requires the fewest evolutionary changes.

Molecular clock

Using the number of sequence differences, calibrated with fossils, to estimate when lineages split.

Check yourself

Try answering in your head before you open each answer.

• 1.On a tree, crocodiles and birds share a node that lizards branched off before. A friend says, "That can't be right: crocodiles look like lizards, not birds." How would you answer?Show answerHide

  Relatedness depends on how recently species share a common ancestor, not on how alike they look. Crocodiles and birds share a more recent ancestor than either does with lizards. Birds changed a great deal after that split, while crocodiles kept more of the ancestral body shape. Their shared derived characters and DNA sequences, not overall appearance, support the grouping.

• 2.Three species are compared at a 100-base stretch of DNA. A and B differ at 3 positions, A and C at 12, and B and C at 11. Which two are sister taxa, and why?Show answerHide

  A and B. They have the fewest differences, so they are most likely to share the most recent common ancestor. C branched off earlier, which is why it's roughly equally different from both.

• 3.Penguins' flippers and seals' flippers are both used for swimming. Are they homologous or analogous? Is there any sense in which they're homologous?Show answerHide

  As flippers, they're analogous: penguins and seals evolved swimming limbs separately, from a flying bird ancestor and a walking mammal ancestor. But as forelimbs, they're homologous, because both are built from the same arm bones inherited from a four-limbed ancestor.