The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae)

Abstract

Museums hold most of the world's most valuable biological specimens and tissues collected, including type material that is often decades or even centuries old. Unfortunately, traditional museum collection and storage methods were not designed to preserve the nucleic acids held within the material, often reducing its potential viability and value for many genetic applications. High‐throughput sequencing technologies and associated applications offer new opportunities for obtaining sequence data from museum samples. In particular, target sequence capture offers a promising approach for recovering large numbers of orthologous loci from relatively small amounts of starting material. In the present study, we test the utility of target sequence capture for obtaining data from museum‐held material from a speciose mammalian genus: the horseshoe bats (Rhinolophidae: Chiroptera). We designed a ‘bait’ for capturing > 3600 genes and applied this to 10 species of horseshoe bat that had been collected between 93 and 7 years ago and preserved using a range of methods. We found that the mean recovery rate per species was approximately 89% of target genes with partial sequence coverage, ranging from 3024 to 3186 genes recovered. On average, we recovered 1206 genes with ≥ 90% sequence coverage, per species. Our findings provide good support for the application of large‐scale bait capture across congeneric species spanning approximately 15 Myr of evolution. On the other hand, we observed no clear association between the success of capture and the phylogenetic distance from the bait model, although sample sizes precluded a formal test.

Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

“…The regions targeted are typically those that are well conserved across the taxa of interest, such as exons and ultraconserved elements (UCEs), so that only a single probe set is required to be designed for the group(s) of interest. These target-based approaches have been applied to a variety of taxa and specimen ages (for example: Bi et al, 2013;Staats et al, 2013;Bailey et al, 2016;Blaimer, Lloyd, Guillory, & Brady, 2016;Prosser, Dewaard, Miller, & Hebert, 2016), and have proven relatively successful in recovering the regions of interest for phylogenomic studies. Despite these advances, application of these methods requires prior genetic knowledge of the taxa of interest in order to facilitate probe design.…”

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

“…For example, sequence capture approaches have been applied to museum specimens >100 years of age in bats [11], birds [12], mammals [8,13,14], insects [10], and plants and fungi [6]. One issue, especially for small insects, is that degradation of DNA quality within a sample not only leads to fragmentation of DNA but also reduces DNA extraction yield [15].…”

Collections-based research in the genomic era

“…In the case of plants, NGS techniques have even succeeded with herbarium specimens preserved in alcohol in the field prior to drying (the so‐called Schweinfurth technique, widely used in the tropics where field drying is difficult; Bridson & Forman, ), which until now were very difficult to sequence due to their low DNA yields (Särkinen et al ., ). In this special issue, seven milestone publications provide detailed laboratory and bioinformatic protocols to reconstruct organellar genomes from historical collections across the animal (horseshoe bats: Bailey et al ., ; insects: Timmermans et al ., ; pigeons: Besnard et al ., ), fungal (Dentinger et al ., ) and plant (angiosperms: Bakker et al ., ; palms: Heyduk et al ., ; olive family: Zedane et al ., ) kingdoms. These pioneering studies provide us with a toolbox for exploiting an almost limitless genetic resource that has been out of reach until now.…”

“…This challenge was the focus of a meeting at the Linnean Society of London (UK) on 2–3 April 2014. The eleven contributions published in this special issue encapsulate the outcome of this fruitful event, and are wide‐ranging in their use of collections in ancient DNA research (Linderholm, ), evolution (Kidner et al ., ), bioinformatics (Vieira et al ., ), phylogenomics (Dodsworth et al ., ; Heyduk et al ., ), systematics (Dentinger et al ., ; Zedane et al ., ) and museomics (Bailey et al ., ; Bakker et al ., ; Besnard et al ., ; Timmermans et al ., ). In this short opinion, we touch on the primary themes explored in this meeting while sharing some of our own views on the subject, especially in relation to the incredible potential of NGS to reinvent collections‐based research.…”