Case Study: Targeted high-Throughput Sequencing of Mitochondrial Genomes from Extinct Cave Bears via Direct Multiplex PCR Sequencing (DMPS)

Here I describe the use of a recently developed technique for targeted high-throughput sequencing of highly degraded DNA by direct multiplex PCR sequencing (DMPS) that was used to amplify 31 near-complete mitochondrial genomes of the extinct cave bear (Ursus spelaeus) . DMPS couples multiplex PCR with the generation of barcoded sequencing libraries to be sequenced in parallel on a high-throughput sequencing platform. DMPS makes it possible to generate large amounts of targeted DNA sequence data simultaneously from multiple degraded samples such as fossil remains. In this chapter, I describe an experiment that uses DMPS with different primer sets and on both modern and ancient DNA templates.