Predictors of sequence capture in a large-scale anchored phylogenomics project

Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method produce reduced representation libraries NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize pre-selected regions genome are via culminating in dataset numerous orthologous loci taxa. Phylogenetic analyses using these sequences potential resolve deep shallow phylogenetic relationships. Identifying factors affect capture success could save time, money, valuable might destructively sampled despite low likelihood success. We investigated impacts specimen age, preservation method, concentration on (number captured quality) while accounting taxonomy extracted tissue type large-scale butterfly project. This project used two probe sets extract 391 subset 13 over 6,000 found resilient capable amplifying samples varying age (0–111 years), (alcohol, papered, pinned), (0.020 ng/?l - 316 ng/ul). Regression demonstrate positively correlated concentration. However, negatively sample method. Our findings suggest projects should prioritize use alcohol-preserved younger than 20 years old when available. In absence such specimens, dried any yield data, albeit returns diminish increasing age.