Species diversity is declining, due to habitat loss, over-exploitation, pollution, and climate change. It is imperative that biodiversity and distributions be accounted for immediately, to understand the impacts of anthropogenic change, and to sustain natural resources. Biodiversity in the seas, and geographic variation, have been underestimated—due to challenges in (1) the delimitation of species, (2) a preponderance of cryptic species, (3) uneven sampling effort, and (4) limited systematic framework. As a consequence, the mechanisms that govern species richness in the seas are poorly understood. The magnitude of these issues varies by taxon and by region, leaving open questions such as: Are estimates of species richness accurate? What are the tempo and mode of evolution in marine species? What mechanisms determine species’ distributions in the ocean?

Here, we tackle the first question, using the example of jellyfishes in the Tropical Eastern Pacific (TEP). The TEP is known as a ‘hotspot’ for its generally high biodiversity, but it harbors only five scyphozoan jellyfishes. To redress the four known challenges facing estimates of marine biodiversity, we increased sampling effort, combined molecular and morphological characters, and applied phylogenetic, barcoding, and morphospecies analyses to estimate species richness of scyphomedusae in the TEP. We found a total of 25 species; of which 22 are new to science, two are non-indigenous, and one is a previous record. Thus, by overcoming known challenges, we found that, as for other more well-known taxa, the TEP also is a hotspot for scyphozoans. To answer the second question, above, we test the hypotheses about the origins of the Discomedusae by synthesizing molecular and morphological phylogenies. We calibrate a scyphozoan molecular clock using geologic events and fossil records. We demonstrate that Coronatae is sister taxon to Discomedusae; we find evidence for geographic radiations in the genus Stomolophus and Family Pelagiidae, which are the most species rich taxa in the TEP. Their diversification rates confirm a rapid genetic radiation in the genera Chysaora, but the morphological characters mapped in the phylogeny did not show any shift in the rates of morphological evolution. To address the last question, we took advantage of a comparative phylogenetic approach. A multi-taxon comparison—including five species of Stomolophus and four Chrysaora species—demonstrates that biological factors play the more important role in shaping species’ distributions and assemblages, compared to abiotic factors. The vicariance model of speciation is not the only process though which the biodiversity in the TEP could have originated. Peripatric and sympatric models of speciation also can define many of the diversification patterns in the TEP.