SNP development in North American burying beetles (Coleoptera: Silphidae): a tool to inform conservation decisions
2015
Houston, Derek D. | Mitchell, Kevin S. | Clouse, Jared W. | Maughan, Peter J. | Curtis Creighton, J. | Smith, Ashlee N. | Bybee, Seth M. | Belk, Mark C.
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.
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