Abstract:

Wildlife biologists collected skin and blubber samples from common bottlenose dolphins (Tursiops truncatus) near Dauphin Island, Alabama during capture/release health assessments and near Mississippi Sound, Mississippi using remote biopsies. We performed DNA sequencing on these samples, targeting a portion of the mitochondrial DNA control region and determined their haplotype for this region. We also genotyped 43 nuclear microsatellite loci. The actual mitochondrial DNA sequence data can be found by searching for the accession numbers provided at https://www.ncbi.nlm.nih.gov/genbank/.

Suggested Citation:

Nicole Vollmer, Patricia Rosel, Keith Mullin, Lori Schwacke, Brian Balmer, Kevin Barry, Anthony Martinez, Brian Quigley, Carrie Sinclair, Todd Speakman, Jesse Wicker, Lynsey Wilcox, Eric Zolman. 2020. Microsatellite genotyping and mitochondrial control region sequencing of skin samples from common bottlenose dolphins (Tursiops truncatus) during remote biopsy surveys near Mississippi Sound, Mississippi from 2018-09-19 to 2018-10-31 and health assessments near Dauphin Island, Alabama from 2018-09-20 to 2018-09-28. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-b3k5-zb33

Purpose:

These data will be used to determine to which stock dolphins that were caught and released as part of the CARMMHA health assessments belong to, as several dolphin stocks are present in the Mobile Bay area. Scientists will use archived samples from animals known to be from the Mississippi Sound Bay, Sound, and Estuary Stock or the Northern Coastal Stock for reference.

Data Parameters and Units:

FieldID Unique identifier for each dolphin sample Collection Date Date of sample collection (m/d/y) Latitude Latitudinal geographic coordinates from the collection location in decimal degrees Longitude Longitudinal geographic coordinates from the collection location in decimal degrees Sex Sex of dolphin (M/F). If sample was collected by remote biopsy, sex was determined using genetic analysis. If sample was collected by health assessment, sex was determined by veterinarians handling the animals. Haplotype Unique mitochondrial control region sequence identifier GenBankAccession# GenBank Accession number Ref Citation where data are reported. See below for full citations. Ttr04_bin1 Allele 1 for microsatellite locus Ttr04 Ttr04_bin2 Allele 2 for microsatellite locus Ttr04 Ttr19_bin1 Allele 1 for microsatellite locus Ttr19 Ttr19_bin2 Allele 2 for microsatellite locus Ttr19 Ttr11_bin1 Allele 1 for microsatellite locus Ttr11 Ttr11_bin2 Allele 2 for microsatellite locus Ttr11 Ttr48_bin1 Allele 1 for microsatellite locus Ttr48 Ttr48_bin2 Allele 2 for microsatellite locus Ttr48 Ttr34_bin1 Allele 1 for microsatellite locus Ttr34 Ttr34_bin2 Allele 2 for microsatellite locus Ttr34 Ttr63_bin1 Allele 1 for microsatellite locus Ttr63 Ttr63_bin2 Allele 2 for microsatellite locus Ttr63 Ttr58_bin1 Allele 1 for microsatellite locus Ttr58 Ttr58_bin2 Allele 2 for microsatellite locus Ttr58 EV37_bin1 Allele 1 for microsatellite locus EV37 EV37_bin2 Allele 2 for microsatellite locus EV37 TxVt5_bin1 Allele 1 for microsatellite locus TxVt5 TxVt5_bin2 Allele 2 for microsatellite locus TxVt5 EV14_bin1 Allele 1 for microsatellite locus EV14 EV14_bin2 Allele 2 for microsatellite locus EV14 EV94_bin1 final Allele 1 for microsatellite locus EV94 EV94_bin2 final Allele 2 for microsatellite locus EV94 MK6_bin1 Allele 1 for microsatellite locus MK6 MK6_bin2 Allele 2 for microsatellite locus MK6 MK8_bin1 Allele 1 for microsatellite locus MK8 MK8_bin2 Allele 2 for microsatellite locus MK8 MK9_bin1 Allele 1 for microsatellite locus MK9 MK9_bin2 Allele 2 for microsatellite locus MK9 KWM12a_bin1 Allele 1 for microsatellite locus KWM12a KWM12a_bin2 Allele 2 for microsatellite locus KWM12a MK5_bin1 Allele 1 for microsatellite locus MK5 MK5_bin2 Allele 2 for microsatellite locus MK5 TxVt7_bin1 Allele 1 for microsatellite locus TxVt7 TxVt7_bin2 Allele 2 for microsatellite locus TxVt7 FF6_bin1 Allele 1 for microsatellite locus FF6 FF6_bin2 Allele 2 for microsatellite locus FF6 PPHO130-bin1 Allele 1 for microsatellite locus PPHO130 PPHO130-bin2 Allele 2 for microsatellite locus PPHO130 Ttr36(tetra)_bin1 Allele 1 for microsatellite locus Ttr36(tetra) Ttr36(tetra)_bin2 Allele 2 for microsatellite locus Ttr36(tetra) Ttr54_bin1 Allele 1 for microsatellite locus Ttr54 Ttr54_bin2 Allele 2 for microsatellite locus Ttr54 Ttr55_bin1 Allele 1 for microsatellite locus Ttr55 Ttr55_bin2 Allele 2 for microsatellite locus Ttr55 Ttr61_bin1 Allele 1 for microsatellite locus Ttr61 Ttr61_bin2 Allele 2 for microsatellite locus Ttr61 Ttr90_bin1 Allele 1 for microsatellite locus Ttr90 Ttr90_bin2 Allele 2 for microsatellite locus Ttr90 Ttr98_bin1 Allele 1 for microsatellite locus Ttr98 Ttr98_bin2 Allele 2 for microsatellite locus Ttr98 Ttr100_bin1 Allele 1 for microsatellite locus Ttr100 Ttr100_bin2 Allele 2 for microsatellite locus Ttr100 Ttr12_bin1 Allele 1 for microsatellite locus Ttr12 Ttr12_bin2 Allele 2 for microsatellite locus Ttr12 Ttr20_bin1 Allele 1 for microsatellite locus Ttr20 Ttr20_bin2 Allele 2 for microsatellite locus Ttr20 Ttr41_bin1 Allele 1 for microsatellite locus Ttr41 Ttr41_bin2 Allele 2 for microsatellite locus Ttr41 Ttr51_bin1 Allele 1 for microsatellite locus Ttr51 Ttr51_bin2 Allele 2 for microsatellite locus Ttr51 Ttr52_bin1 Allele 1 for microsatellite locus Ttr52 Ttr52_bin2 Allele 2 for microsatellite locus Ttr52 DL1_bin1 Allele 1 for microsatellite locus DL1 DL1_bin2 Allele 2 for microsatellite locus DL1 Ttr56_bin1 Allele 1 for microsatellite locus Ttr56 Ttr56_bin2 Allele 2 for microsatellite locus Ttr56 Ttr83_bin1 Allele 1 for microsatellite locus Ttr83 Ttr83_bin2 Allele 2 for microsatellite locus Ttr83 D08_bin1 Allele 1 for microsatellite locus D08 D08_bin2 Allele 2 for microsatellite locus D08 D22_bin1 Allele 1 for microsatellite locus D22 D22_bin2 Allele 2 for microsatellite locus D22 Dde70_bin1 Allele 1 for microsatellite locus Dde70 Dde70_bin2 Allele 2 for microsatellite locus Dde70 Ttr71_bin1 Allele 1 for microsatellite locus Ttr71 Ttr71_bin2 Allele 2 for microsatellite locus Ttr71 Ttr78_bin1 Allele 1 for microsatellite locus Ttr78 Ttr78_bin2 Allele 2 for microsatellite locus Ttr78 Ttr84_bin1 Allele 1 for microsatellite locus Ttr84 Ttr84_bin2 Allele 2 for microsatellite locus Ttr84 DL3_bin1 Allele 1 for microsatellite locus DL3 DL3_bin2 Allele 2 for microsatellite locus DL3 DL12_bin1 Allele 1 for microsatellite locus DL12 DL12_bin2 Allele 2 for microsatellite locus DL12 SW19_bin1 Allele 1 for microsatellite locus SW19 SW19_bin2 Allele 2 for microsatellite locus SW19

Methods:

For each sample, a 354 bp portion of the mitochondrial control region was amplified using the polymerase chain reaction (PCR). Subsequently, DNA sequences were determined using either an ABI 3130 or 3500 Genetic Analyzer, edited in Sequencher 5.4.6 (Gene Codes Corporation) and then aligned by eye in Geneious Prime 2020.0.05 to identify unique mitochondrial DNA haplotypes. Also, all samples were amplified at 43 nuclear microsatellite loci using the Type-it Microsatellite PCR Kit (Qiagen) and genotyped using either the ABI 3130 or 3500 Genetic Analyzer and the appropriate internal size standard. The program GeneMapper v6.0 (ABI) was used to determine allele sizes for all loci.

Provenance and Historical References:

Kingston, S. E., Adams, L. D., & Rosel, P. E. (2009). Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae). BMC Evolutionary Biology, 9(1), 245. doi:10.1186/1471-2148-9-245 Sellas, A. B., Wells, R. S., & Rosel, P. E. (2005). Mitochondrial and nuclear DNA analyses reveal fine scale geographic structure in bottlenose dolphins (Tursiops truncatus) in the Gulf of Mexico. Conservation Genetics, 6(5), 715–728. doi:10.1007/s10592-005-9031-7 Vollmer, N. L., & Rosel, P. E. (2017). Fine-scale population structure of common bottlenose dolphins (Tursiops truncatus) in offshore and coastal waters of the US Gulf of Mexico. Marine Biology, 164(8). doi:10.1007/s00227-017-3186-x

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