Targeted sequencing of ancient horses using CNERs

We develop a cost-effective DNA bait synthesis method named Circular Nucleic acid Enrichment Reagent synthesis (CNERs, pronounced as snares) to overcome disadvantages of current bait making processes. Using CNERs, we genotype 23,771 SNPs in ten Late Pleistocene caballine horse samples recovered from the holarctic permafrost. Up to 98.3% of the targeted SNPs are recovered with 16x median coverage for high endogenous samples. We further demonstrate that targeted genotyping with the CNERs method is a cost-effective and reliable approach for inferring population structure and demographic history in degraded ancient samples.