Molecular phylogenetics of the Clupeiformes based on exon-capture data and a new classification of the order

The sequence alignment or 1,165 loci of 66 clupeiform species and five outgroups. The loci were filtered for more than 70% taxa having sequences for each locus. Analyzing the data, we reconstructed a robust phylogeny of the Clupeiformes based on thousands of nuclear coding sequences obtained through target enrichment and curated for phylogenetic informativeness. We confirmed that the Clupeiformes is monophyletic, and Denticeps is sister to the Clupeoidei. Dussumieriids in their former understanding are polyphyletic, as Spratelloididae being sister to all other clupeoids. Sundasalanx belongs to Ehiravidae, but with deep split to other ehiravine species. A time tree of the Clupeiformes was calibrated with new fossil data and an updated classification of the Clupeiformes is provided.