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. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society,
2016