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How to read a phylogenetic tree
The drawing is a hypothesis about kinship. It is not a family portrait with a direction of improvement.
Trees are how biology draws genealogy once there are too many cousins for a paragraph. They are easy to read wrongly with great confidence. Four habits prevent most of the damage.
The tips are not a sequence
The ends of the branches are the organisms or the genes being compared. Their left-to-right or top-to-bottom order is a convenience of the drawing. You can spin a branch around its node and the hypothesis does not change. A bacterium drawn at the left is not “before” a human drawn at the right. Both tips are in the present unless the figure explicitly says a tip is a fossil.
A node is a population, not a fossil we failed to find
An internal node is the inferred common ancestor of the branches that descend from it. It is not, automatically, a named extinct species that someone hopes to dig up. Sometimes a fossil can be placed on a tree. The tree does not owe you that fossil. What it owes you is a claim about who shares a more recent ancestor with whom.
Time runs from the root, not from left to right
If the tree has a root, the root is the oldest point on that drawing. Branch length may mean time, or the amount of change, or nothing quantitative at all. The caption is required to say which. A longer branch is not a more important organism. It is often a lineage in which the measured characters changed more, or a lineage that has been evolving for longer, and those are different statements.
Nobody is more evolved
Every living tip has had the same amount of time since the root. Sharks are not behind mammals. Bacteria are not an early draft of you. A parasite with a stripped genome can be exquisitely adapted and look “simple” on a checklist written by someone who loves organs. Natural selection, on the concepts page, has no ladder. A tree that seems to show one has been turned so that our species sits at the end. Turn it back.
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