Utility of single nucleotide polymorphism (SNP) markers for genetic species identification of pallid and shovelnose sturgeon

The pallid sturgeon is an endangered species endemic to the Missouri and Mississippi river drainages. Pallid sturgeon are found sympatrically throughout their entire range with the more common shovelnose sturgeon. Range wide, pallid and shovelnose are very similar morphologically, therefore DNA markers are useful for discriminating between them. Currently, microsatellites are the most commonly used DNA marker to differentiate between the species; however they suffer from various technical and analytical problems, and are expensive to score. Single Nucleotide Polymorphisms (SNP)s have emerged as an alternative marker for species identification. SNP markers have the advantage of being relatively cheap, standardized, and have the potential for high throughput analysis. We have characterized several SNP loci, which exhibit very different allele frequencies between pallid and shovelnose sturgeon in the northern part of the range with decreasing differences in allele frequencies in the southern part of the range.  These trends are coincident with decreasing morphological, microsatellite, and mitochondrial DNA differentiation cited in previous studies. While the markers developed so far are very effective for differentiating species in the northern part of the range, additional SNP loci will be required for better species resolution in the southern part of the range.