Museum ‘omics

Museums serve as libraries of biodiversity on Earth. How this library is utilized has changed with advanced imaging technologies and the internet, permitting widespread digitization and dissemination of data. Similarly sequencing technology has revealed potential to unlock the genetic biodiversity in these collections, often in cases when the specimens were not collected with genetic data in mind. The utility of museum specimens for phylogenetics has been widely recognized since Sanger sequencing of individually amplified loci began to be used as a tool in phylogenetics, though often this has relied heavily on freshly collected material. I am involved in two collaborative projects sequencing the genomes of scorpions: the i5k project, which published the genome for Centruroides sculpturatus, and the California Conservation Genomics Project which is in the final stages of a chromosomal-level genome for Uroctonus mordax. Results of this research have already highlighted that a whole genome duplication occurred in the shared common ancestor of scorpions and spiders. The Urcotonus mordax project will represent the most complete genome for scorpions to date, and will help taxonomically place an iconic species in California that is currently not able to be confidently assigned to a family. Over the past decade, pipelines using archival museum specimens have been developed for a variety of types of genomic data useful in phylogenomics, though in many cases, destructive sampling is necessary to obtain DNA. I have been working on new methods for increasing the utility of archival specimens in phylogenomic studies, including the development of new UCE probes targeting mites, and the use of mini-barcodes to affirm morphological associations of specimens. However, by obtaining whole-genome data from museum specimens, instead of a few loci using Sanger sequencing, we are able to maximize the data we can access from these specimens. We have been harvesting ultraconserved elements in silico (computationally) from low-coverage whole genome sequencing data, and propose this approach will provide a model for successfully extracting UCE loci and legacy Sanger loci in tandem, and further allow for future use of genomic information like functional genes under selection that may not be used for phylogenetic inference.

Funding: California Insect Barcoding and Workforce Development, California Institute of Biodiversity. ARTS: Taxonomy and Molecular Systematics of Mesh Web Spiders (Araneae: Dictynidae), National Science Foundation DEB-2026623 to Crews, Esposito, and Spagna.