DOI: 10.5061/dryad.29ds0
title: Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays

description: Although single nucleotide polymorphisms (SNPs) are commonly used in human
 genetics, they have only recently been incorporated into genetic studies
 of non-model organisms, including cetaceans. SNPs have several advantages
 over other molecular markers for studies of population genetics: they are
 quicker and more straightforward to score, cross-laboratory comparisons of
 data are less complicated, and they can be used successfully with
 low-quality DNA. We screened portions of the genome of one of the most
 abundant cetaceans in U.S. waters, the common bottlenose dolphin (Tursiops
 truncatus), and identified 153 SNPs resulting in an overall average of one
 SNP every 463 base pairs. Custom TaqMan® Assays were designed for 53 of
 these SNPs and their performance was tested by genotyping a set of
 bottlenose dolphin samples, including some with low quality DNA. We found
 that in 19% of the loci examined, the minor allele frequency (MAF)
 estimated during initial SNP ascertainment using a DNA pool of 10
 individuals differed significantly from the final MAF after genotyping
 over 100 individuals, suggesting caution when making inferences about MAF
 values based on small data sets. For two assays, we also characterised the
 basis for unusual clustering patterns to determine whether their data
 could still be utilised for further genetic studies. Overall results
 support the use of these SNPs for accurate analysis of both poor and good
 quality DNA. We report the first SNP markers and genotyping assays for use
 in population and conservation genetic studies of bottlenose dolphins.
description: T.truncatus COL3A1-like
 geneSequence alignment file
 (.fasta) presenting sequencing results of five T. truncatus individuals of
 the DNA pool for the collagen type III alpha 1-like gene (COL3A1). There
 is one SNP in this fragment. Four individuals were sampled in the Gulf of
 Mexico and one in the western North Atlantic. Sequences were derived using
 an ABI 3130 and aligned in the program Se-Al. All work was completed at
 the Southeast Fisheries Science Center (SEFSC) Marine Mammal Molecular
 Genetics Lab (MMMGL).T.truncatus GRP78-like
 geneSequence alignment file
 (.fasta) presenting sequencing results of five T. truncatus individuals of
 the DNA pool for the glucose-regulated protein 78kDa-like gene (GRP78).
 There is one SNP in this fragment. Four individuals were sampled in the
 Gulf of Mexico and one in the western North Atlantic. Sequences were
 derived using an ABI 3130 and aligned in the program Se-Al. All work was
 completed at the Southeast Fisheries Science Center (SEFSC) Marine Mammal
 Molecular Genetics Lab (MMMGL).T.trunatus GLB1-like
 geneSequence alignment file
 (.fasta) presenting sequencing results of five T. truncatus individuals of
 the DNA pool for the galactosidase beta 1-like gene (GLB1). There is one
 SNP in this fragment. Four individuals were sampled in the Gulf of Mexico
 and one in the western North Atlantic. Sequences were derived using an ABI
 3130 and aligned in the program Se-Al. All work was completed at the
 Southeast Fisheries Science Center (SEFSC) Marine Mammal Molecular
 Genetics Lab (MMMGL).