Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays

Citation

Cruz VP, Vera M, Pardo BG, Taggart J, Martinez P, Oliveira C & Foresti F (2017) Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays. Molecular Ecology Resources, 17 (3), pp. 550-556. https://doi.org/10.1111/1755-0998.12564

Abstract
Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226774 reads (65.5Mb) were obtained (mean read length 289±183bp) detecting a total of 5399 contigs (mean contig length: 396±91bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty-two of these SNPs were successfully validated and 61 were polymorphic: 14 in P.falkneri, 21 in P.motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.

Keywords
conservation tools; genetic fish; hybridization; NGS techniques; Potamotrygon ; SNPs

Journal
Molecular Ecology Resources: Volume 17, Issue 3