Ladybirds (family Coccinellidae) are one of the most diverse groups of beetles and globally comprise over 6000 species. Despite their scientific and economic significance, the taxonomy of Coccinellidae remains unstable, and we still know little about their evolutionary history. By using a small number of genes, previous phylogenetic analyses have not reliably resolved the relationships among major ladybird lineages. In this study, we sequenced 94 nuclear protein-coding genes for 214 species of Coccinellidae and 14 outgroups, covering 90 genera and 35 tribes. We found that the nucleotide compositional heterogeneity is present between ladybird tribes so that phylogenetic inference at the amino acid level is more reliable. Based on the maximum likelihood analyses of the amino acid dataset, we recognized three subfamilies in Coccinellidae: Microweisinae, Monocoryninae, and Coccinellinae. The subfamily relationships are strongly supported as (Microweisinae, (Monocoryninae, Coccinellinae)). The tribes of ladybirds are mostly monophyletic, except Ortaliini, Sticholotidini, Scymnini, and Coccidulini. The phylogenetic relationships among tribes of Coccinellinae were still not resolved yet, with many nodes weakly supported. Our divergence time analysis suggests that the crown group of extant lady beetles occurred in the Early Cretaceous ~143 million years ago (Mya) and experienced a rapid diversification process during the Late Cretaceous (120 - 70 Mya). We hypothesize that that the boom of angiosperms in the Late Cretaceous may promote the diversification of herbivorous Sternorrhyncha insects, especially aphids, which in turn drove the rapid radiation of predatory lady beetles. In summary, our work provides a comprehensive time-calibrated phylogeny of Coccinellidae that provides a sound framework for revising their classification and understanding the origin of their biodiversity.
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