Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Abstract

Abstract. Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31 Chrysomeloidea, four outgroup taxa: two Curculionoidea and two Cucujoidea) included exemplars of all families and 23 of 30 subfamilies of Chrysomeloidea (18 of 19 non-chrysomelid Chrysomeloidea), with a focus on the large family Cerambycidae. Our results reveal a monophyletic Cerambycidae s.s. in all but one analysis, and a polyphyletic Cerambycidae s.l. When monophyletic, Cerambycidae s.s. was sister to the family Disteniidae. Relationships among the subfamilies of Cerambycidae s.s. were also recovered with strong statistical support except for Cerambycinae being made paraphyletic by Dorcasomus Audinet-Serville (Dorcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon -Chrysomelidae, Disteniidae, Vesperidae and Orsodacnidae -were monophyletic, but Megalopodidae was rendered paraphyletic by Cheloderus Gray (Oxypeltidae). Our study corroborates some relationships within Chrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon-sampled, phylogenetic and evolutionary studies of the families and subfamilies of Cerambycidae s.l. and other Chrysomeloidea.

Museum specimens provide phylogenomic data to resolve relationships of sack‐bearer moths (Lepidoptera,Mimallonoidea,Mimallonidae)

“…High‐throughput targeted sequencing approaches in phylogenetics have become central to understanding the evolutionary history of diverse branches of the tree of life. These methodologies, such as anchored hybrid enrichment (AHE) and ultra‐conserved elements (UCEs), are now regularly being applied to phylogenetic studies on plants and animals (including both invertebrates and vertebrates), resulting in robustly supported trees that are answering fundamental questions of evolution, biogeography and systematics (Crawford et al ., ; Faircloth et al ., , ; Prum et al ., ; Hamilton et al ., ; Young et al ., ; Dietrich et al ., ; Fragoso‐Martínez et al ., ; Maddison et al ., ; Wanke et al ., ; Winterton et al ., ; Breinholt et al ., ; Espeland et al ., ; Haddad et al ., ). These methods are believed to work better than traditional Sanger‐based PCR on degraded samples because high‐throughput sequencing technologies are more effective at sequencing fragmented DNA sequences (Lemmon et al ., ; Blaimer et al ., ).…”

Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers

“…Anchored hybrid enrichment (AHE) targeting ultra-conserved elements (UCEs) is an NGS technique that uses oligonucleotide probes to capture conserved regions of the genome flanked by less conserved areas in order to acquire useful data for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, such approach is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost (Young et al, 2016, Haddad et al, 2017. Therefore, such genome assembly-free methods are becoming preferential choices in the systematics field, especially in large-scale phylogenetics projects.…”

Morphological and Molecular Perspectives on the Phylogeny, Evolution, and Classification of Weevils (Coleoptera: Curculionoidea): Proceedings from the 2016 International Weevil Meeting

“…AHE is a method of sequencing known targeted genes (here, known 1:1 orthologs) using probes, the design of which is taxon-specific. In this presentation, the workflow and general concept of AHE were presented (see [12,45] for more information on the probes and our evolving analytical pipeline). Using our AHE probes we can obtain DNA sequence data from up to approximately 500 genes for each taxon of interest.…”

“…Additionally, he discussed the kinds of molecular data (e.g., genomes, transcriptomes, anchored hybrid enrichment, ultraconserved elements) that his lab is currently using to reconstruct beetle phylogeny and he shared information about several different target enrichment probe sets under development in his lab for studying beetle phylogeny and evolution. These included the probes currently being used across the Phytophaga (including the 1K Weevils project [12] and studies of Scolytinae [23] as well as ongoing studies of longhorned beetles [45] and Buprestidae) and new probe sets under development specifically for use in the Phytophaga.…”

“…This is especially true among the higher Curculionidae. The 1K Weevils Project seeks to infer a molecular phylogeny and chronogram (timetree) for the family Curculionidae using phylogenomic data (1000 species,~500 genes [45]), thereby further establishing Curculionoidea as a model system for testing predictions and refining general theories about the evolution of insect-plant interactions. A corresponding morphological study (detailed in a talk by Dave Clarke) will permit independent reconstruction of curculionid phylogeny and assessment of curculionid morphology in light of the results from analysis of these and the molecular data.…”