Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens

PLoS One. 2016 Aug 24;11(8):e0161531. doi: 10.1371/journal.pone.0161531. eCollection 2016.

Abstract

Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.

MeSH terms

  • Animals
  • Computational Biology / methods
  • Conserved Sequence*
  • Genome Components*
  • Genome, Insect*
  • Insecta / classification*
  • Insecta / genetics*
  • Phylogeny
  • Sequence Analysis, DNA*

Grant support

Funding for this study was provided by the Smithsonian Institution Competitive Grants Program for Science and a Smithsonian Global Genome Initiative (www.ggi.si.edu) grant (to SGB). WXG was supported by an NHRE summer research internship for undergraduates funded by the NSF-REU program (grant number EAR-1062692, awarded to Elizabeth Cottrell and Gene Hunt). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.