Dating nodes on molecular phylogenies: a critique of molecular biogeography

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Abstract
Taxa have been dated using three methods: equating their age with the age of the oldest known fossil, with the age of strata the taxa are endemic to, and with the age of paleogeographic events. All three methods have been adopted as methods of dating nodes in molecular phylogenies. The first method has been the most popular, but both this and the second method involve serious difficulties. Studies often, correctly, introduce oldest known fossils as providing minimum ages for divergences. However, in the actual analyses these ages, and ages derived from them, are often treated as absolute ages and earlier geological events are deemed irrelevant to the phylogeny. In fact, only younger geological events can be irrelevant. Studies correlating the age of nodes with age of volcanic islands often overlook the fact that these islands have been produced at subduction zones or hot spots where small, individually ephemeral islands are constantly being produced and disappearing, and a metapopulation can survive indefinitely. Correlating the age of taxa with that of associated paleogeographic events is probably the most promising method but has often been used in a simplistic way, for example in assuming that all divergence across the Isthmus of Panama dates to its final rise. Most workers now agree that a global molecular clock does not exist, and that rates can change between lineages and within a lineage over time. New methods of estimating branch lengths do not assume a strict clock, but the number of models for molecular evolution is then effectively infinite. Problems with calibrating the nodes, as well as with substitution models, mean that phylogeography's claim to be able to test between vicariance and dispersal is not justified.