HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Abstract

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained with inmorethana billionbiological specimensdepositedinnatural historymuseums remains recalcitrant toanalysisowing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraintshinderingourabilitytoaddressmajorevolutionaryquestions.WeaddressedthisimpedimentbydevelopingphyloHyRAD,a newbioinformaticpipelineenablinglocusrecoveryatabroadevolutionaryscalefromHyRAD-Xexomecaptureofmuseumspecimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens.Our newpipeline can also successfully align rawRNAseq transcriptomic and ultraconserved element readswith theRADderivedprobecatalog. Usingthismethod,wegeneratedarobusttimetreeforCarabinaebeetles, thelackofwhichhadprecludedstudy ofmacroevolutionarytrendspertainingtotheirbiogeographyandwing-morphologyevolution.Wesuccessfully recoveredupto2,945 lociwith amean of 1,788 loci across the exome of specimens of varying age.Coveragewas not significantly linked to specimen age, demonstrating thewideexploitabilityofmuseumspecimens.Wealso recoveredfragmentary mitogenomes compatiblewithSangersequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct AplothoraxWaterhouse, 1841 nestedwithin the genus CalosomaWeber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.