A phylogenomic tree inferred with an inexpensive <scp>PCR</scp>‐generated probe kit resolves higher‐level relationships among <i>Neptis</i> butterflies (Nymphalidae: Limenitidinae)

<jats:title>Abstract</jats:title><jats:p>Recent advances in obtaining reduced representation libraries for next‐generation sequencing permit phylogenomic analysis of species‐rich, recently diverged taxa. In this study, we performed sequence capture with homemade PCR‐generated probes to study diversification among closely related species in a large insect genus to examine the utility of this method. We reconstructed the phylogeny of <jats:italic>Neptis</jats:italic> Fabricius, a large and poorly studied nymphalid butterfly genus distributed throughout the Old World. We inferred relationships among 108 <jats:italic>Neptis</jats:italic> samples using 89 loci totaling up to 84 519 bp per specimen. Our taxon sample focused on Palearctic, Oriental and Australasian species, but included 8 African species and outgroups from 5 related genera. Maximum likelihood and Bayesian analyses yielded identical trees with full support for almost all nodes. We confirmed that <jats:italic>Neptis</jats:italic> is not monophyletic because <jats:italic>Lasippa heliodore</jats:italic> (Fabricius) and <jats:italic>Phaedyma amphion</jats:italic> (Linnaeus) are nested within the genus, and we redefine species groups for <jats:italic>Neptis</jats:italic> found outside of Africa. The statistical support of our results demonstrates that the probe set we employed is useful for inferring phylogenetic relationships among <jats:italic>Neptis</jats:italic> species and likely has great value for intrageneric phylogenetic reconstruction of Lepidoptera. Based on our results, we revise the following two taxa: <jats:italic>Neptis heliodore</jats:italic> <jats:bold>comb. rev.</jats:bold> and <jats:italic>Neptis amphion</jats:italic> <jats:bold>comb.</jats:bold> <jats:bold>rev.</jats:bold></jats:p>