Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae) q Nathanael D. Herrera a,⇑ , Jan Johan ter Poorten b,c , Rüdiger Bieler c , Paula M. Mikkelsen d , Ellen E. Strong e , David Jablonski f , Scott J. Steppan a a Department of Biological Science, Florida State University, Tallahassee, FL 32304, United States b Naturalis Biodiversity Center, P.O. Box 9517, Leiden, Netherlands c Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, United States d Paleontological Research Institution, and Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14850, United States e Smithsonian Institution, National Museum of Natural History, Washington, DC 20013, United States f Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, United States article info Article history: Received 30 December 2014 Revised 2 July 2015 Accepted 18 July 2015 Available online 30 July 2015 Keywords: Bayesian Biodiversity Dispersal–extinction–cladogenesis Fossil Marine Mollusca abstract Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most exten- sive examination of model-based historical biogeography among marine invertebrates to date. We con- ducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal–extinction–cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC recon- struction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions. Ó 2015 Elsevier Inc. All rights reserved. 1. Introduction Understanding the historical forces shaping biodiversity is an important aspect of marine biogeography, but one that lags behind terrestrial studies. The latitudinal diversity gradient, with high spe- cies diversity in the tropics and a decrease toward the poles, is one of the fundamental patterns of biological diversity on the planet (Hillebrand, 2004), and is found in many groups from terrestrial angiosperms to marine mollusks (Crame, 2000; Willig et al., 2003; Jablonski et al., 2006, 2013). The longitudinal decline in marine species richness has also spurred much debate (Briggs, 2003; Cox and Moore, 2010) but is less well understood. Central to these issues are hypotheses describing the origin and mainte- nance of faunal diversity throughout the marine realm. Much of the debate has focused on whether the tropics, especially the west- ern Pacific, are a center of origin, or sink (accumulation) of diver- sity (Rocha et al., 2008). Although much attention has been focused on the Indo-Pacific, there have been few attempts to explore global patterns of origination, dispersal, and accumulation between the major marine biogeographic regions (Cowman et al., 2013). Several challenges exist for these studies, such as the lack of discrete physical barriers between the major marine realms. Further, dispersal via planktonic larvae has obscured the patterns of connectivity and origin of marine species (Cowman et al., 2013). Therefore, it is evident that a detailed assessment of global patterns of dispersal and origination among the major marine http://dx.doi.org/10.1016/j.ympev.2015.07.013 1055-7903/Ó 2015 Elsevier Inc. All rights reserved. q This paper was edited by the Associate Editor Jan Strugnell. ⇑ Corresponding author. E-mail addresses: nherrera@bio.fsu.edu, ndh04c@gmail.com (N.D. Herrera), terpoorten@chello.nl (J.J. ter Poorten), rbieler@fieldmuseum.org (R. Bieler), pmm37@cornell.edu (P.M. Mikkelsen), StrongE@si.edu (E.E. Strong), djablons@ uchicago.edu (D. Jablonski). Molecular Phylogenetics and Evolution 93 (2015) 94–106 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev