AFSC/RACE/EcoFOCI - Genetics analyses performed in support of FOCI assessment surveys and ecosystem observations in the Bering Sea and the Gulf of Alaska 2009 - 2010

The datasets contain nucleotide sequence data that is in text format and each line of sequence has a unique sample code (combination of letters and numbers).

These datasets were developed to fulfill two NPRB funded projects, one to determine the utility of simple, low-cost genetic methods for identifying species of prey fish in the diets of groundfish and the other to collect sequence data from common and rare species of sculpins that would likely be present in groundfish stomach contents. These data are for research purposes.

Supplemental Information - Data Parameters and Units - Descriptive Information about the Data Parameters and Units.

The data itself is descriptive providing a unique string of DNA sequence and presented in this raw form. The data are archival species references for later post-processing. No parameters were measured or included.

Supplemental Information – Methods - Descriptive Information about the methods used.

[Are you sure you want methods starting with the DNA extraction? The paper that this passage was taken from is written for scientists who would like to repeat the genetic methods at the bench so is written as a laboratory protocol. Seems like you might just limit this section to how the sequence data was generated in very abbreviated terms such as the following:

PCR products from fish samples were sequenced using ABI Big Dye chemistry version 3.1 (Applied Biosystems, Inc) and run on an ABI 3730 automated sequencer. KB BASECALLER quality scores were generated using ABI data collection software version 3.0, and bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Both directions were sequenced and aligned for reference specimen samples that showed intraspecific variation in RFLP banding patterns; otherwise, sequence from one direction was analyzed for PCR-RFLP assay development. Likewise, DNA sequence from one direction was analyzed for prey samples not assigned to one of the target fish groups (i.e. that could not be identified using the PCR-RFLP protocols), or were classified as unknown teleosts. Replicate DNA extractions of 12 prey items were sequenced in order to verify consistency of sequence data between replicates and to test for contamination from other prey species. Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/). Sequences from samples that could not be identified using the PCR-RFLP protocols, or that were classified as unknown teleosts, were compared to the database of reference sequences in GenBank using the BLAST (Basic Local Alignment Search Tool) query algorithm.]

Supplemental Information – Instruments - Descriptive Information about the instruments and equipment used.

PCR products from fish samples were run on an ABI 3730 automated sequencer (Applied Biosystems, Inc).

Supplemental Information - Sampling Scales and Rates - Descriptive Information about the sampling spatial and temporal scales and rates.

Sampling included the Northeast Pacific and was conducted opportunistically over multiple years.

Supplemental Information - Error Analysis - Descriptive Information about the error analysis.

PCR products from fish samples were run on an ABI 3730 automated sequencer and KB BASECALLER quality scores were generated using ABI data collection software version 3.0. Bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Matching haplotypes among samples confirmed correct species identification of voucher specimens.

Supplemental Information - Provenance and Historical References -

Descriptive Information about the provenance, historical data, key information packaged elsewhere.

Paquin, M.M., Buckley, T.W., Hibpshman, R. E., and Canino, M.F. (2014) DNA-based identification methods of prey fish from stomach contents of 12 species of eastern North Pacific groundfish. Deep Sea Research I 85:110-117.

Paquin, M.M., Kagley, A.N., Fresh K.L., and Orr, J.W. (2014) First Records of the Night Smelt, Spirinchus starksi, in the Salish Sea, Washington. Northwestern Naturalist, 95:40-43. 2014.

There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed.

Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/).

User must read and fully comprehend the metadata prior to use. Applications or inferences derived from the data should be carefully considered for accuracy.

Acknowledgement of NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested.

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PCR products from fish samples were sequenced using ABI Big Dye chemistry version 3.1 (Applied Biosystems, Inc) and run on an ABI 3730 automated sequencer. KB BASECALLER quality scores were generated using ABI data collection software version 3.0, and bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Both directions were sequenced and aligned for reference specimen samples that showed intraspecific variation in RFLP banding patterns; otherwise, sequence from one direction was analyzed for PCR-RFLP assay development. Likewise, DNA sequence from one direction was analyzed for prey samples not assigned to one of the target fish groups (i.e. that could not be identified using the PCR-RFLP protocols), or were classified as unknown teleosts. Replicate DNA extractions of 12 prey items were sequenced in order to verify consistency of sequence data between replicates and to test for contamination from other prey species. Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/). Sequences from samples that could not be identified using the PCR-RFLP protocols, or that were classified as unknown teleosts, were compared to the database of reference sequences in GenBank using the BLAST (Basic Local Alignment Search Tool) query algorithm.]