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Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Michael G Harvey1, Brian Tilston Smith2, Travis C Glenn3

  • 1Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA, mharve9@lsu.edu.

Systematic Biology
|June 12, 2016
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Summary

Sequence capture offers better data comparability for shallow systematics than RAD-Seq, making it ideal for comparative phylogeography. RAD-Seq is cost-effective but has limitations in marker overlap and data consistency across studies.

Keywords:
Allele frequency spectrumbirdscoalescent methods; concordance analysismassively parallel sequencingnext-generation sequencingultraconserved elements

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Area of Science:

  • Genomics
  • Systematics
  • Bioinformatics

Background:

  • Restriction site associated DNA sequencing (RAD-Seq) is widely used for shallow timescale studies, but its limitations compared to sequence capture are underexplored.
  • Both RAD-Seq and sequence capture are genomic enrichment strategies for next-generation sequencing in systematics.

Purpose of the Study:

  • To discuss the limitations and benefits of RAD-Seq and sequence capture for shallow systematics in non-model species.
  • To compare the utility of RAD-Seq and sequence capture by re-analyzing data from Xenops minutus.

Main Methods:

  • Review of prior studies utilizing RAD-Seq and sequence capture.
  • Re-analysis of existing RAD-Seq and sequence capture datasets from Xenops minutus.
  • Comparative analysis of marker dispersion, data quality, and orthology assessment between methods.

Main Results:

  • RAD-Seq offers widely dispersed markers, cost-effectiveness, and deep coverage but suffers from low marker overlap and sensitivity to heterozygosity, compromising comparability.
  • Sequence capture provides flexibility, targets specific genomic regions, works with low-quality DNA, and allows for straightforward orthology assessment, enhancing comparability.
  • Sequence capture of conserved regions enables consistent locus interrogation across divergent species, crucial for comparative studies.

Conclusions:

  • Sequence capture is advantageous for maintaining data comparability across studies in shallow systematics and comparative phylogeography.
  • Sequence capture should be more widely considered for obtaining data in systematics and comparative phylogeography due to its strengths in cross-study comparability.
  • While RAD-Seq is valuable for its cost and marker density, sequence capture offers superior long-term utility for broad systematic and phylogeographic inferences.