Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles?

Hume B Douglas,Jackson Eyres,Adam J Brunke,Adam Ślipiński,Karine Savard,Julie T Chapados,Jeremy R Dettman,Hermes E Escalona,Robin Richter,Duane Mckenna,Robin Kundrata

doi:10.3390/biology10060451

Abstract

Simple SummaryIn the era of phylogenomics, new molecular sequencing and computational techniques can aid in resolving phylogenetic relationships that were previously intractable by morphological or limited molecular data. In this study, we used anchored hybrid enrichment—designed to recover DNA sequences from hundreds of single-copy orthologous genes—to resolve the phylogeny of the Elateridae (click-beetles) and establish their placement within superfamily Elateroidea. The resulting data were compatible with published transcriptomes, allowing for integrating our dataset with previously published data. Using a wide range of analyses on these molecular data, we tested hypotheses long-debated in the morphological literature and also the robustness of our phylogenetic inferences. Our results placed the bioluminescent lampyroids (fireflies and relatives) within the click-beetles, challenging the current classification of Elateridae, Lampyridae, Phengodidae, and Rhagophthalmidae. However, despite the large amount of molecular data analyzed, a few nodes with conflicting phylogenetic signals could not be unambiguously resolved. Overall, we recovered well-resolved tree topologies that will serve as a framework for further systematic and evolutionary studies of click-beetles. This work further demonstrates that the click-beetle lineage contains not only pest wireworms, but also many species that benefit agriculture.Click-beetles (Coleoptera: Elateridae) are an abundant, diverse, and economically important beetle family that includes bioluminescent species. To date, molecular phylogenies have sampled relatively few taxa and genes, incompletely resolving subfamily level relationships. We present a novel probe set for anchored hybrid enrichment of 2260 single-copy orthologous genes in Elateroidea. Using these probes, we undertook the largest phylogenomic study of Elateroidea to date (99 Elateroidea, including 86 Elateridae, plus 5 non-elateroid outgroups). We sequenced specimens from 88 taxa to test the monophyly of families, subfamilies and tribes. Maximum likelihood and coalescent phylogenetic analyses produced well-resolved topologies. Notably, the included non-elaterid bioluminescent families (Lampyridae + Phengodidae + Rhagophthalmidae) form a clade within the otherwise monophyletic Elateridae, and Sinopyrophoridae may not warrant recognition as a family. All analyses recovered the elaterid subfamilies Elaterinae, Agrypninae, Cardiophorinae, Negastriinae, Pityobiinae, and Tetralobinae as monophyletic. Our results were conflicting on whether the hypnoidines are sister to Dendrometrinae or Cardiophorinae + Negastriinae. Moreover, we show that fossils with the eucnemid-type frons and elongate cylindrical shape may belong to Eucnemidae, Elateridae: Thylacosterninae, ancestral hard-bodied cantharoids or related extinct groups. Proposed taxonomic changes include recognition of Plastocerini as a tribe in Dendrometrinae and Hypnoidinae stat. nov. as a subfamily within Elateridae.

Highlights

Elateridae, with over 11,000 species distributed in all zoogeographical regions, are among the largest and most diverse beetle families (Figure 1), and elaterid species collectively exhibit a diversity of trophic habits—perhaps more than any other beetle family [1].Their crown group and taxonomic diversification can be traced back to the Mesozoic, their precise age remains uncertain [2,3,4,5,6]
While we briefly describe probe design here, full probe design methodology, scripts and the probe set itself can be found at https://github.com/AAFC-BICoE/Elateridaeortholog-baitset
In addition to strong evidence from the present phylogenomic analyses, we find this result convincing because Tetralobinae were viewed as sister to, or part of, Agrypninae based on adult and larval morphology [70] and phylogenetic analysis of adult morphology [9] and because the same trees are congruent with the placement of Hypnoidini based on morphological evidence

Summary

Introduction

Elateridae, with over 11,000 species distributed in all zoogeographical regions, are among the largest and most diverse beetle families (Figure 1), and elaterid species collectively exhibit a diversity of trophic habits—perhaps more than any other beetle family [1]. Their crown group and taxonomic diversification can be traced back to the Mesozoic, their precise age remains uncertain [2,3,4,5,6]. The classification of Elateridae is in disarray with several conflicting systems, which contributes to the challenge of taxonomic and applied research on its many poorly known species. Efforts to resolve the subfamily level phylogeny of click-beetles using morphology [8,9]

Methods

Results

Discussion

Conclusion