Anchored phylogenomics illuminates the skipper butterfly tree of life

Abstract

BackgroundButterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families.MethodsTo infer a robust phylogenomic hypothesis for Hesperiidae, we sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers. Molecular datasets were analyzed using maximum-likelihood, parsimony and coalescent multi-species phylogenetic methods.ResultsAll analyses converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all nodes and all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as the sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within the grass skippers (Hesperiinae), there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a subfamily, are recovered as monophyletic with strong support, but are deeply nested within Hesperiinae.ConclusionsAnchored Hybrid Enrichment sequencing resulted in a large amount of data that built the foundation for a new, robust evolutionary tree of skippers. The newly inferred phylogenetic tree resolves long-standing systematic issues and changes our understanding of the skipper tree of life. These resultsenhance understanding of the evolution of one of the most species-rich butterfly families.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1216-z) contains supplementary material, which is available to authorized users.

Out of the Orient: Post‐Tethyan transoceanic and trans‐Arabian routes fostered the spread of Baorini skippers in the Afrotropics

“…The placement of Baorini within Hesperiinae remains unclear due to the staggering diversity of the subfamily (> 2000 described species) and the lack of a comprehensive phylogeny for this group. However, recent phylogenomic evidence (Toussaint et al , ) suggests that Baorini might be part of a large phylogenetic grade, thereby rendering difficult the inclusion of outgroups that might inform the estimation of ancestral ranges (Toussaint & Short, ). Our biogeobears analysis recovers an origin of Baorini in the Oriental region plus Greater Sunda Islands/Philippines.…”

“…Samples of 32 Baorini species were collected in the field (Appendix S1) and placed in glassine envelopes or directly in > 95% ethanol. In the laboratory, DNA was extracted from abdomens or legs using an OmniPrep™ DNA extraction kit (G‐Biosciences, Saint‐Louis, MO, U.S.A.) following Toussaint et al (). Quantified DNA extracts were submitted to RAPiD Genomics (Gainesville, FL, U.S.A.) for library preparation, hybridization enrichment, and sequencing.…”

“…When possible, we built chimeras between newly sequenced specimens and other specimens of the same species for which other sequence data were available to improve sequence coverage for terminals. We included 19 skipper outgroups from all subfamilies and major clades (Toussaint et al , ) to allow the use of secondary calibrations. All sequence data were imported into geneious r8.1.…”

“…Gene trees were inferred using fasttree 2.1.5 (Price et al , ) and inspected for contamination and sequence quality. Trees were rooted with Macrosoma hyacinthina Warren (Hedylidae), as the Hedylidae are the sister group to the Hesperiidae (Espeland et al , ; Toussaint et al , ). The final matrix included 89 species, including 70 Baorini, and 16 concatenated loci, totalling up to 12 928 aligned nucleotides.…”

“…However, because relationships among Coeliadinae genera and their monophyly are uncertain, any placement of the fossil elsewhere than on the stem of Coeliadinae remains contentious (de Jong, , ). Therefore, because Coeliadinae is sister to the remainder of Hesperiidae (Espeland et al , ; Toussaint et al , ), the fossil would only calibrate a minimum age of 55 Ma for crown Hesperiidae, while Espeland et al () estimated this node to be c . 76 Ma and the split between Hesperiidae and Hedylidae to be c .…”