Anchored Hybrid Enrichment (AHE) is a rapid and cost-effective high-throughput sequencing approach capable of generating multi-locus datasets for phylogenomics. These datasets are comprised of pre-selected regions of the genome that can be used to resolve phylogenetic relationships at varying evolutionary timescales. An added benefit of this technique is its ability to amplify sequence data from degraded DNA which is often associated with museum specimens. Determining what impacts successful sequence capture could inform future anchored phylogenomics projects to save time, money, and valuable specimens-especially if a phylogenomics project plans to include museum samples. To determine the predictors of successful sequence capture we investigated the impact of specimen age, preservation method, and DNA concentration on capture in a large-scale butterfly phylogenomics project that employed two AHE probe sets. We find that AHE is a robust method capable of amplifying sequences in samples of varying age (0-111 years), preservation method (ethanol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Our findings also show that sequence capture is positively correlated with DNA concentration and negatively correlated with sample age and preservation method. Sequence capture projects should therefore prioritize the use of ethanol-preserved specimens younger than 20 years old when possible.
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