At the most basic level, phylogenetic trees represent hypotheses about evolutionary history. For example, the tree at left below represents the hypothesis that chimpanzees and bonobos are very closely related to one another and that, of the groups shown, humans are their closest living relatives. The tree at the right represents an alternative hypothesis, that gorillas are the closest relatives of chimpanzees and bonobos.
Like any good hypothesis, an evolutionary tree is based on logic, background knowledge, and most importantly, evidence. For example, chimpanzees share many more genetic similarities with humans than they do with gorillas.1 Independent research has uncovered strong genetic evidence supporting the tree at the left above and suggesting that the hypothesis shown on the right should be rejected.2 All things considered, the tree at left does a better job of explaining the available evidence and so is accepted by scientists as an accurate hypothesis for the time being.
Feeling lost? Review tree basics with the primer.
For examples of how trees change with new evidence, see our page on this topic in the Primer.
1Scally, A., J.Y. Dutheil, L.W. Hillier, G.E.Jordan, I. Goodhead, J. Herrero, … and R. Durbin. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.
2King, M.C., and A.C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.