ABSTRACT
Scientists have been studying ancient DNA for three decades, but next-generation sequencing (NGS) has made the process of sequencing ancient DNA much easier. This technological leap has huge potential for genomic analysis of the very museum specimens that already form the foundation of prior knowledge about biodiversity. We are still determining which methods of preparing ancient DNA for NGS work best for various questions, especially with regard to whether whole genomes need to be sequenced or whether a subset of the genome is more desirable and computationally tractable. In this chapter, we discuss different methods for preparing ancient DNA for NGS, and various analytical issues specific to NGS data output from ancient DNA sources. We focus mainly on birds and discuss several case studies where NGS has been applied to very old museum specimens, like subfossils, as well as younger specimens, like those from museum study skins collected in the last century. Although few recently published studies using NGS are about ancient DNA from bird museum specimens, the number is expected to grow rapidly. The case studies demonstrate that systematics and taxonomy are important applications of NGS to museum specimens, and that plenty remains to be learned from specimens about population-level processes such as the genetics of changes in population size, some of which have led to extinction. Better methods of extracting ancient DNA from museum specimens are badly needed, as well as careful consideration of how the research community archives DNA extractions and the billions of DNA sequencing reads now being produced from museum specimens on NGS platforms. Methods for correcting errors that occur during NGS, as well as those introduced during the process of DNA degradation in the specimen itself (e.g., deamination), are in development, but easy-to-use pipelines are still lacking. In sum, although methods are still in development, the field of next-generation museum genomics is burgeoning, with high potential to extend the utility of museum specimens in bird systematics, historical demography, and conservation.
