Data and code from: Synthesis of molecular data on Mactroidea (Bivalvia): phylogenetic implications and open questions

Abstract Molecular phylogenetics have clarified high-level evolutionary relationships across the tree of life but sampling is highly uneven at lower levels, particularly for marine organisms. Here, we synthesize all publicly available Sanger sequence data for the diverse but under-sampled marine bivalve superfamily Mactroidea to provide a unified molecular and paleontological framework, and to guide targeted sampling to elucidate the group’s evolutionary history. We infer two complementary phylogenetic estimates, one using a comprehensive eight-gene alignment that maximizes taxon sampling, and a second high-coverage three-gene alignment that maximizes molecular coverage. Both phylogenies are largely concordant with morphology-based classifications at the genus and subgenus levels, but reveal that the three recognized mactroid families and the subfamilies of Mactridae are not reciprocally monophyletic. Among the genera, evidence suggests that Pseudocardium is not in the present-day fauna, and that Coelomactra, Longimactra, Spisulona, and Taria, often synonymized to various extant taxa, may be valid genera or subgenera, although further molecular data are needed to confirm these taxonomic implications. Budding-informed time-calibration using 27 fossil constraints reveals several conflicts between fossil ages and the inferred molecular topology, likely owing to incomplete fossil and molecular sampling and ambiguity of certain fossil assignments. By tabulating conflicting or missing data, we identify priorities for future molecular sampling, and show that gaps in the molecular data are unevenly distributed geographically, with concentrations in the East Pacific and New Zealand. Combined phylogenetic, biogeographic, and paleontologic inventories, supported by voucher-based verification of specimens, can guide targeted sampling to efficiently improve understanding of within-clade relationships and evolutionary dynamics in Mactroidea.