Conservation Genetics Resources

, Volume 7, Issue 2, pp 349–352 | Cite as

SNP development in North American burying beetles (Coleoptera: Silphidae): a tool to inform conservation decisions

  • Derek D. Houston
  • Kevin S. Mitchell
  • Jared W. Clouse
  • Peter J. Maughan
  • J. Curtis Creighton
  • Ashlee N. Smith
  • Seth M. Bybee
  • Mark C. Belk
Technical Note

Abstract

We used genomic and bioinformatic techniques to identify single nucleotide polymorphisms (SNPs) for use in population genetic studies and conservation efforts of North American burying beetles. Genomic reduction, barcoding, 454-pyrosequencing and de novo assembly of the resultant reads yielded 30,399 large contigs (>400 bp) for us to scrutinize. We identified 10,992 putative SNPs in DNA sequences of the burying beetle Nicrophorus orbicollis, and from those we developed a panel of 96 highly polymorphic SNP assays. We validated the 96 SNP assays on a diversity panel of 95 individuals using KASPar genotyping chemistry detected using the Fluidigm dynamic array platform. 53 of the 96 SNP assays (55 %) were clearly polymorphic across N. orbicollis samples, with 28 in Hardy–Weinberg equilibrium. These SNPs can be used to assess population demographic parameters of N. orbicollis populations, then those data may be used to inform conservation efforts of its sister species, the endangered N. americanus.

Keywords

SNP genotyping Next-generation sequencing Population genomics Burying beetles 

Supplementary material

12686_2015_438_MOESM1_ESM.pdf (85 kb)
Online Resource 1: Table containing sequences for the 96 SNP primer assays used in this study (PDF 86 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Derek D. Houston
    • 1
  • Kevin S. Mitchell
    • 2
  • Jared W. Clouse
    • 3
  • Peter J. Maughan
    • 3
  • J. Curtis Creighton
    • 4
  • Ashlee N. Smith
    • 2
  • Seth M. Bybee
    • 2
  • Mark C. Belk
    • 2
  1. 1.Department of Ecology Evolution and Organismal BiologyIowa State UniversityAmesUSA
  2. 2.Department of BiologyBrigham Young UniversityProvoUSA
  3. 3.Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUSA
  4. 4.Department of Biological SciencesPurdue University CalumetHammondUSA

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