02695nas a2200253 4500008004100000245012300041210006900164520190900233653003102142653001702173653001502190653002602205653001402231100001502245700001302260700001702273700001702290700001502307700001602322700002002338700001602358700001802374856004902392 2017 eng d00aAnchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)0 aAnchored hybrid enrichment provides new insights into the phylog3 a

"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."

10aANCHORED HYBRID ENRICHMENT10aCERAMBYCIDAE10aCOLEOPTERA10aHIGHER CLASSIFICATION10aPHYLOGENY1 aHaddad, S.1 aShin, S.1 aLemmon, A.R.1 aLemmon, E.M.1 aSvacha, P.1 aFarrell, B.1 aŚlipiński, A.1 aWindsor, D.1 aMcKenna, D.D. uhttps://sphingidae.myspecies.info/node/2157803368nas a2200277 4500008004100000245012100041210006900162520252600231653003102757653001302788653002602801653001602827653001602843653001802859653001402877653001302891653001602904653001502920100002002935700001302955700001702968700002402985700001303009700001903022856004903041 2017 eng d00aResolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics0 aResolving relationships among the megadiverse butterflies and mo3 a

"The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target “probe” region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels.We combineAHEand transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea + Gelechioidea + Thyridoidea) + (Papilionoidea + Pyraloidea + Macroheterocera). To examine the efficacy of AHE at a shallowtaxonomic level, phylogenetic analyseswere also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community."

10aANCHORED HYBRID ENRICHMENT10aHEMARINI10aHIGHER CLASSIFICATION10aLEPIDOPTERA10aMETHODOLOGY10aPHYLOGENOMICS10aPHYLOGENY10aPIPELINE10aSATURNIIDAE10aSPHINGIDAE1 aBreinholt, J.W.1 aEarl, C.1 aLemmon, A.R.1 aMoriarty_Lemmon, E.1 aXiao, L.1 aKawahara, A.Y. uhttps://sphingidae.myspecies.info/node/21525