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 within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae ...摘要 系统发育基因组学（phylogenomics）的进展有助于解决长期悬而未决的演化问题。然而，存放于自然历史博物馆中的十亿余份生物标本所蕴含的遗传多样性，因其本身的DNA降解特性而难以开展分析。不过这一极具潜力的资源，对于克服阻碍我们解答重大演化问题的类群采样瓶颈至关重要。为此，我们开发了phyloHyRAD——一款全新的生物信息学流程，可借助由高DNA完整性标本开发的台式RAD来源的外显子组复杂度降低探针组，对低DNA完整性的博物馆标本开展HyRAD-X外显子组捕获，并在宽泛的演化尺度上实现位点恢复。该流程还可成功将原始RNAseq转录组测序reads与超保守元件测序reads比对至RAD来源的探针目录中。借助该方法，我们为步甲亚科（Carabinae）构建了一棵稳健的时间树……