Data from: A comprehensive and dated phylogenomic analysis of butterflies

Butterflies (Papilionoidea), with over 18,000 described species [1], have
captivated naturalists and scientists for centuries. They play a central
role in the study of speciation, community ecology, biogeography, climate
change, and plant-insect interactions and include many model organisms and
pest species [2, 3]. However, a robust higher-level phylogenetic framework
is lacking. To fill this gap, we inferred a dated phylogeny by analyzing
the first phylogenomic dataset, including 352 loci (> 150,000 bp)
from 207 species representing 98% of tribes, a 35-fold increase in gene
sampling and 3-fold increase in taxon sampling over previous studies [4].
Most data were generated with a new anchored hybrid enrichment (AHE) [5]
gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g.,
[6]) informative loci, enabling direct comparison and future dataset
merging with previous studies. Butterflies originated around 119 million
years ago (mya) in the late Cretaceous, but most extant lineages diverged
after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses
support swallowtails (Papilionidae) as sister to all other butterflies,
followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae)
as sister to the remainder, indicating a secondary reversal from
diurnality to nocturnality. The whites (Pieridae) were strongly supported
as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks
(Lycaenidae and Riodinidae). Ant association independently evolved once in
Lycaenidae and twice in Riodinidae. This study overturns prior notions of
the taxon’s evolutionary history, as many long-recognized subfamilies and
tribes are para- or polyphyletic. It also provides a much-needed backbone
for a revised classification of butterflies and for future comparative
studies including genome evolution and ecology.