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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.
Figure 1. Phylogeny of Encope and the other genera of Mellitidae based on concatenated COI, ATPase-6, ATPase-8, 16S and 28S data reconstructed with MrBayes and RAxML and rooted on L. sexiesperforata. Clade credibility values >75% of Maximum Likelihood (first number next to node) and >85% of Bayesian (second number) reconstruction are shown. Numbers after locality names indicate individuals with indistinguishable haplotypes, scale bar reflects number of changes per site. Names next to terminal branches indicate the morphology of the specimens; names to the right of the pictures are our interpretation as to species affiliation according to the molecular phylogeny. Colors represent geographic range (red = Atlantic and Caribbean, blue = eastern Pacific, green = Gulf of California, black = unknown). Aboral club-spine structures (lateral view) are shown next to subclades in E. micropora.
Figure 2. Bayesian estimates of median molecular divergence times (dates next to nodes) based on concatenated COI, ATPase-6, ATPase-8, 16S, and 28S data, as derived from analysis using BEAST and calibrated using the fossil record. Black dots indicate temporally constrained nodes. Images of fossils indicate the oldest known occurrence of each constrained species. Bars indicate 95% Highest Posterior Density (HPD) limits. The fossil designated E. sp. 1 is the undescribed species from the Gatun Formation mentioned in the text. Ages of stages and epoch series are based on International Commission on Stratigraphy stratigraphic chart90 (Aquit. = Aquitanian, Lang. = Langhian, Serr. = Serravallian, Mes. = Messinian, Za. = Zanclean, Pi. = Piacenzian, Plio. = Pliocene, G. = Gelasian, C. = Calabrian, M. = Middle, Pleist. = Pleistocene). Error bars represent 95% Highest Posterior Density (HPD) intervals.
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