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Vicariant events have been widely used to calibrate rates of molecular evolution, the completion of the Central American Isthmus more extensively than any other. Recent studies have claimed that rather than the generally accepted date of ~3 million years ago (Ma), the Isthmus was effectively complete by the middle Miocene, 13 Ma. We present a fossil calibrated phylogeny of the new world sand dollar genus  Encope , based on one nuclear and four mitochondrial genes, calibrated with fossils at multiple nodes. Present day distributions of  Encope  are likely the result of multiple range contractions and extinction events. Most species are now endemic to a single region, but one widely distributed species in each ocean is composed of morphotypes previously described as separate species. The most recent separation between eastern Pacific and Caribbean extant clades occurred at 4.90 Ma, indicating that the Isthmus of Panama allowed genetic exchange until the Pliocene. The rate of evolution of mitochondrial genes in  Encope  has been ten times slower than in the closely related genera  Mellita  and  Lanthonia . This large difference in rates suggests that splits between eastern Pacific and Caribbean biota, dated on the assumption of a “universal” mitochondrial DNA clock are not valid.

Phylogeography of the sand dollar genus Encope: implications regarding the Central American Isthmus and rates of molecular evolution