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Title: Discovery of 20,000 RAD-SNPs and development of a 52-SNP array for monitoring river otters

Author: Stetz, Jeffrey B.; Smith, Seth; Sawaya, Michael A.; Ramsey, Alan B.; Amish, Stephen J.; Schwartz, Michael K.; Luikart, Gordon;

Date: 2016

Source: Conservation Genetics Resources. doi: 10.1007/s12686-016-0558-3.

Publication Series: Scientific Journal (JRNL)

Description:

Many North American river otter (Lontra canadensis) populations are threatened or recovering but are difficult to study because they occur at low densities, it is difficult to visually identify individuals, and they inhabit aquatic environments that accelerate degradation of biological samples. Single nucleotide polymorphisms (SNPs) can improve our ability to monitor demographic and genetic parameters of difficult to study species. We used restriction site associated DNA (RAD) sequencing to discover 20,772 SNPs present in Montana, USA, river otter populations, including 14,512 loci that were also variable in at least one other population range-wide. After applying careful filtering criteria meant to minimize ascertainment bias and identify high quality, highly heterozygous (Ho = 0.2-0.50) SNPs, we developed and tested 52 independent SNP qPCR genotyping assays, including 41 that performed well with diluted DNA. The 41 loci provided high power for population assignment tests with only 1 misassignment (1.6 %) between closely neighboring populations. Our SNPs showed high power to differentiate individuals and assign them to population of origin, as well as strong concordance of genotypes from high and diluted concentrations of DNA, and between original RAD and the SNP qPCR array.

Keywords: conservation genomics, RAD, next generation sequencing, river otter, SNP, population monitoring, noninvasive genetic tagging

Publication Notes:

  • We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
  • This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.

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Citation:


Stetz, Jeffrey B.; Smith, Seth; Sawaya, Michael A.; Ramsey, Alan B.; Amish, Stephen J.; Schwartz, Michael K.; Luikart, Gordon. 2016. Discovery of 20,000 RAD-SNPs and development of a 52-SNP array for monitoring river otters. Conservation Genetics Resources. doi: 10.1007/s12686-016-0558-3.

 


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