New dates and new rates for divergence across the Isthmus of Panama

Sister species separated by the Isthmus of Panama have been widely used to estimate rates of molecular evolution. These estimates are based on the ass umption that geographic isolation occurred nearly simultaneously for most t axa, when connections between the Caribbean and eastern Pacific closed appr oximately three million years ago. Here we show that this assumption is inv alid for the only genus for which many taxa and multiple genetic markers ha ve been analysed. Patterns of divergence exhibited by allozymes and the mit ochondrial COI gene are highly concordant for 15 pairs of snapping shrimp i n the genus Alpheus, indicating that they provide a reasonable basis for es timating time since cessation of gene flow The extent of genetic divergence between pairs of sister species varied over fourfold. Sister species from mangrove environments showed the least divergence, as would be expected if these were among the last habitats to be divided. Using this pair yields a rate of sequence divergence of 1.4% per one million years, with implied tim es of separation for the 15 pairs of 3-18 million years ago. Many past stud ies may have overestimated rates of molecular evolution because they sample d pairs that were separated well before final closure of the Isthmus.